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/7786831/working'
mkdir: created directory `/scratch/stefan/7786831/working/protonate'
Storing results in /scratch/stefan/7786831/finished
Working in /scratch/stefan/7786831/working
/scratch/stefan/7786831/working /scratch/stefan/7786831

/scratch/stefan/7786831/working/protonate /scratch/stefan/7786831/working /scratch/stefan/7786831
Precomputing protomers for all compounds (pH: 7.4)
ph 7.4: 1084 protomers created
Coalesing and merging protomers
1043 protomers generated for 1000 compounds
Checking for new stereocenters and expanding
1069 protomers after new stereo-center expansion
/scratch/stefan/7786831/working /scratch/stefan/7786831

Bulk generating 3D conformations all protomers in /scratch/stefan/7786831/working/3D
mkdir: created directory `/scratch/stefan/7786831/working/3D'
We are using corina for 3D embeding
debuging info:: /scratch/stefan/7786831/working/protonate/xaaabbi-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'
1070 3D conformations generated for 1000 compounds

Building REAL300025051150
mkdir: created directory `/scratch/stefan/7786831/working/building'
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051150'
/scratch/stefan/7786831/working/building/REAL300025051150 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051150

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051150/0 /scratch/stefan/7786831/working/building/REAL300025051150 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1
`/scratch/stefan/7786831/working/3D/1' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC(C)OCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051150.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051150.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051150/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051150 none CC(C)CC(C)OCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 189, 177, 189, 144, 144, 94, 94, 94, 94, 81, 55, 55, 26, 55, 12, 1, 1, 1, 1, 1, 1, 1, 94, 94, 201, 201, 201, 201, 201, 201, 201, 201, 201, 189, 189, 189, 189, 144, 144, 144, 144, 94, 81, 81, 55, 26, 26, 1, 94, 94, 94, 94] 201
rigid atoms, others: [50, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54])
total number of confs: 798
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051150 none CC(C)CC(C)OCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 31, 31, 26, 15, 26, 8, 8, 2, 2, 2, 1, 1, 1, 4, 7, 7, 7, 25, 40, 94, 94, 94, 94, 94, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 26, 26, 26, 26, 8, 8, 8, 8, 2, 4, 4, 7, 25, 25, 94, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 51, 52, 53, 54, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 319
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051150 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051150
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `/scratch/stefan/7786831/finished'
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051150/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051150
Building REAL300025051151
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051151'
/scratch/stefan/7786831/working/building/REAL300025051151 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051151

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051151/0 /scratch/stefan/7786831/working/building/REAL300025051151 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 2)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/2
`/scratch/stefan/7786831/working/3D/2' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CNC(=O)N1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051151.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051151.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051151/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051151 none O=C(CNC(=O)N1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 8, 1, 11, 8, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 6, 7, 7, 7, 12, 12, 12, 10, 1, 1, 1, 7, 26, 26, 26, 72, 92, 159, 159, 159, 159, 159, 1, 1, 6, 6, 7, 12, 12, 12, 12, 12, 12, 12, 12, 2, 7, 7, 26, 72, 72, 159, 1, 1, 1, 1] 188
rigid atoms, others: [11, 12, 13, 46, 45, 48, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 454
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051151 none O=C(CNC(=O)N1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 8, 1, 11, 8, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [12, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 12, 12, 12, 23, 49, 49, 49, 107, 126, 188, 188, 188, 188, 188, 12, 12, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 12, 23, 23, 49, 107, 107, 188, 12, 12, 12, 12] 188
rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 36, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 592
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051151 none O=C(CNC(=O)N1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 8, 1, 11, 8, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [159, 159, 159, 188, 188, 188, 188, 188, 188, 188, 188, 159, 142, 94, 94, 54, 94, 13, 1, 1, 1, 1, 1, 1, 1, 159, 159, 188, 188, 188, 188, 188, 188, 188, 188, 188, 188, 188, 159, 142, 142, 94, 54, 54, 1, 159, 159, 159, 159] 188
rigid atoms, others: [44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48])
total number of confs: 780
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051151 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051151
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051151/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051151
Building REAL300025051152
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051152'
/scratch/stefan/7786831/working/building/REAL300025051152 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051152

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051152/0 /scratch/stefan/7786831/working/building/REAL300025051152 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 3)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/3
`/scratch/stefan/7786831/working/3D/3' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCOCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051152.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051152.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051152/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051152 none C#CCOCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 159, 133, 133, 81, 81, 81, 81, 74, 54, 54, 31, 54, 13, 1, 1, 1, 1, 1, 1, 1, 81, 81, 201, 201, 201, 133, 133, 133, 133, 81, 74, 74, 54, 31, 31, 1, 81, 81, 81, 81] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41])
total number of confs: 849
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051152 none C#CCOCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [35, 35, 12, 7, 7, 2, 2, 2, 1, 1, 1, 3, 5, 5, 5, 17, 27, 81, 81, 81, 81, 81, 1, 1, 35, 35, 35, 7, 7, 7, 7, 2, 3, 3, 5, 17, 17, 81, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 8, 9, 10, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
total number of confs: 284
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051152 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051152
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051152/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051152
Building REAL300025051153
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051153'
/scratch/stefan/7786831/working/building/REAL300025051153 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051153

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051153/0 /scratch/stefan/7786831/working/building/REAL300025051153 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 4)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/4
`/scratch/stefan/7786831/working/3D/4' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=N1)

`REAL300025051153.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051153.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051153/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051153 none COCCN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 15, 11, 3, 3, 3, 2, 2, 2, 1, 1, 1, 4, 8, 8, 8, 26, 41, 125, 125, 125, 125, 125, 1, 1, 3, 3, 26, 26, 26, 15, 15, 11, 11, 3, 2, 4, 4, 8, 26, 26, 125, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
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: REAL300025051153 none COCCN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 10, 7, 1, 1, 1, 1, 1, 2, 2, 3, 3, 6, 10, 10, 10, 30, 46, 134, 134, 134, 134, 134, 3, 3, 1, 1, 21, 21, 21, 10, 10, 7, 7, 1, 3, 6, 6, 10, 30, 30, 134, 3, 3, 3, 3] 201
rigid atoms, others: [34, 3, 4, 5, 6, 7, 25, 26] set([0, 1, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 325
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051153 none COCCN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 189, 134, 134, 134, 125, 125, 125, 125, 100, 60, 60, 27, 60, 12, 1, 1, 1, 1, 1, 1, 1, 125, 125, 134, 134, 201, 201, 201, 201, 201, 189, 189, 134, 125, 100, 100, 60, 27, 27, 1, 125, 125, 125, 125] 201
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 891
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051153 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051153
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051153/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051153
Building REAL300025051154
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051154'
/scratch/stefan/7786831/working/building/REAL300025051154 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051154

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051154/0 /scratch/stefan/7786831/working/building/REAL300025051154 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 5)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/5
`/scratch/stefan/7786831/working/3D/5' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCOC(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051154.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051154.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051154/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051154 none C#CCOC(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 178, 171, 121, 171, 121, 121, 121, 97, 59, 59, 27, 59, 12, 1, 1, 1, 1, 1, 1, 1, 121, 121, 201, 201, 201, 171, 171, 171, 171, 121, 97, 97, 59, 27, 27, 1, 121, 121, 121, 121] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41])
total number of confs: 926
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051154 none C#CCOC(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 9, 5, 2, 5, 2, 2, 1, 1, 1, 4, 9, 9, 9, 25, 41, 121, 121, 121, 121, 121, 1, 1, 20, 20, 20, 5, 5, 5, 5, 2, 4, 4, 9, 25, 25, 121, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 8, 9, 10, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
total number of confs: 304
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051154 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051154
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051154/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051154
Building REAL300025051155
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051155'
/scratch/stefan/7786831/working/building/REAL300025051155 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051155

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051155/0 /scratch/stefan/7786831/working/building/REAL300025051155 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 6)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/6
`/scratch/stefan/7786831/working/3D/6' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)[N@@H+]1CCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051155.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051155.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051155/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051155 none CC(C)[N@@H+]1CCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 1, 1, 1, 5, 10, 10, 10, 17, 23, 42, 42, 42, 42, 42, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 5, 5, 10, 17, 17, 42, 1, 1, 1, 1] 44
rigid atoms, others: [11, 12, 13, 48, 49, 50, 51, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 122
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051155 none CC(C)[N@@H+]1CCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 14, 14, 14, 22, 30, 44, 44, 44, 44, 44, 6, 6, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 6, 9, 9, 14, 22, 22, 44, 6, 6, 6, 6] 44
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 39, 40, 35, 36, 38, 37] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 124
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051155 none CC(C)[N@@H+]1CCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 42, 42, 42, 42, 41, 39, 39, 21, 39, 12, 1, 1, 1, 1, 1, 1, 1, 42, 42, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 42, 41, 41, 39, 21, 21, 1, 42, 42, 42, 42] 44
rigid atoms, others: [47, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51])
total number of confs: 144
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051155 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051155/1 /scratch/stefan/7786831/working/building/REAL300025051155 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 7)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/7
`/scratch/stefan/7786831/working/3D/7' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)[N@H+]1CCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051155.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051155.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051155/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051155 none CC(C)[N@H+]1CCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 7, 18, 18, 18, 43, 65, 97, 97, 97, 97, 97, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 18, 43, 43, 97, 1, 1, 1, 1] 97
rigid atoms, others: [11, 12, 13, 48, 49, 50, 51, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 270
number of broken/clashed sets: 96
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051155 none CC(C)[N@H+]1CCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 8, 19, 19, 19, 44, 66, 97, 97, 97, 97, 97, 3, 3, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 8, 8, 19, 44, 44, 97, 3, 3, 3, 3] 97
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 39, 40, 35, 36, 38, 37] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 275
number of broken/clashed sets: 96
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051155 none CC(C)[N@H+]1CCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [97, 97, 97, 97, 97, 97, 97, 97, 97, 97, 97, 97, 92, 75, 75, 32, 75, 13, 1, 1, 1, 1, 1, 1, 1, 97, 97, 97, 97, 97, 97, 97, 97, 97, 97, 97, 97, 97, 97, 97, 97, 97, 92, 92, 75, 32, 32, 1, 97, 97, 97, 97] 97
rigid atoms, others: [47, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51])
total number of confs: 356
number of broken/clashed sets: 96
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051155 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051155
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051155/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051155/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051155
Building REAL300025051156
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051156'
/scratch/stefan/7786831/working/building/REAL300025051156 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051156

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051156/0 /scratch/stefan/7786831/working/building/REAL300025051156 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 8)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/8
`/scratch/stefan/7786831/working/3D/8' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCOCC1CC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051156.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051156.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051156/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051156 none O=C(CCOCC1CC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 5, 5, 9, 22, 43, 43, 1, 1, 1, 3, 5, 5, 5, 16, 26, 86, 86, 86, 86, 86, 1, 1, 5, 5, 5, 5, 22, 22, 43, 43, 43, 43, 43, 2, 3, 3, 5, 16, 16, 86, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 46, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 317
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051156 none O=C(CCOCC1CC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [43, 30, 23, 15, 5, 1, 1, 1, 1, 43, 43, 43, 55, 69, 69, 69, 125, 150, 201, 201, 201, 201, 201, 43, 43, 30, 30, 23, 23, 5, 5, 1, 1, 1, 1, 1, 43, 55, 55, 69, 125, 125, 201, 43, 43, 43, 43] 201
rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 31] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 709
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051156 none O=C(CCOCC1CC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [86, 86, 86, 125, 125, 141, 163, 201, 201, 86, 76, 54, 54, 30, 54, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 125, 125, 125, 125, 163, 163, 201, 201, 201, 201, 201, 86, 76, 76, 54, 30, 30, 1, 86, 86, 86, 86] 201
rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46])
total number of confs: 839
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051156 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051156
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051156/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051156
Building REAL300025051157
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051157'
/scratch/stefan/7786831/working/building/REAL300025051157 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051157

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051157/0 /scratch/stefan/7786831/working/building/REAL300025051157 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 9)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/9
`/scratch/stefan/7786831/working/3D/9' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNS(=O)(=O)CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051157.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051157.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051157/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051157 none CNS(=O)(=O)CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 200, 201, 201, 200, 136, 136, 136, 136, 115, 68, 68, 28, 68, 13, 1, 1, 1, 1, 1, 1, 1, 136, 136, 201, 201, 201, 201, 200, 200, 200, 200, 136, 115, 115, 68, 28, 28, 1, 136, 136, 136, 136] 201
rigid atoms, others: [39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 854
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051157 none CNS(=O)(=O)CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 10, 8, 10, 10, 7, 2, 2, 2, 1, 1, 1, 4, 9, 9, 9, 29, 44, 136, 136, 136, 136, 136, 1, 1, 24, 24, 24, 24, 8, 8, 7, 7, 2, 4, 4, 9, 29, 29, 136, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 344
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051157 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051157
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051157/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051157
Building REAL300025051158
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051158'
/scratch/stefan/7786831/working/building/REAL300025051158 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051158

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051158/0 /scratch/stefan/7786831/working/building/REAL300025051158 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 10)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/10
`/scratch/stefan/7786831/working/3D/10' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC1C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1)

`REAL300025051158.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051158.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051158/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051158 none CC1CC1C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 9, 21, 21, 21, 66, 75, 158, 158, 158, 158, 158, 3, 3, 1, 4, 4, 4, 4, 4, 4, 4, 1, 1, 3, 9, 9, 21, 66, 66, 158, 3, 3, 3, 3] 201
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 35, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025051158 none CC1CC1C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 4, 3, 4, 4, 6, 6, 6, 6, 22, 46, 46, 46, 122, 129, 201, 201, 201, 201, 201, 6, 6, 4, 2, 2, 2, 1, 1, 1, 1, 4, 4, 6, 22, 22, 46, 122, 122, 201, 6, 6, 6, 6] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 646
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051158 none CC1CC1C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 158, 158, 158, 158, 157, 157, 157, 157, 98, 43, 43, 25, 43, 12, 1, 1, 1, 1, 1, 1, 1, 157, 157, 158, 201, 201, 201, 201, 201, 201, 201, 158, 158, 157, 98, 98, 43, 25, 25, 1, 157, 157, 157, 157] 201
rigid atoms, others: [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, 40, 41, 43, 44, 45, 46])
total number of confs: 765
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051158 none CC1CC1C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 7, 19, 19, 19, 62, 71, 157, 157, 157, 157, 157, 1, 1, 3, 6, 6, 6, 6, 6, 6, 6, 3, 3, 2, 7, 7, 19, 62, 62, 157, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 403
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051158 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051158
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051158/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051158
Building REAL300025051159
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051159'
/scratch/stefan/7786831/working/building/REAL300025051159 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051159

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051159/0 /scratch/stefan/7786831/working/building/REAL300025051159 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 11)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/11
`/scratch/stefan/7786831/working/3D/11' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1)

`REAL300025051159.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051159.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051159/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051159 none CC(C)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 2, 2, 1, 1, 1, 4, 19, 19, 19, 68, 80, 148, 148, 148, 148, 148, 1, 1, 5, 5, 6, 6, 6, 6, 6, 6, 6, 5, 5, 2, 4, 4, 19, 68, 68, 148, 1, 1, 1, 1, 5] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 46, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47])
total number of confs: 390
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051159 none CC(C)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 5, 5, 5, 11, 50, 50, 50, 125, 144, 201, 201, 201, 201, 201, 5, 5, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 5, 11, 11, 50, 125, 125, 201, 5, 5, 5, 5, 1] 201
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 47, 35, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 628
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051159 none CC(C)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 148, 148, 148, 148, 122, 74, 74, 30, 74, 13, 1, 1, 1, 1, 1, 1, 1, 148, 148, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 148, 122, 122, 74, 30, 30, 1, 148, 148, 148, 148, 201] 201
rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47])
total number of confs: 658
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051159 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051159
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051159/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051159
Building REAL300025051160
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051160'
/scratch/stefan/7786831/working/building/REAL300025051160 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051160

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051160/0 /scratch/stefan/7786831/working/building/REAL300025051160 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 12)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/12
`/scratch/stefan/7786831/working/3D/12' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)[N@@H+]1CCCC1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051160.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051160.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051160/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051160 none CC(C)[N@@H+]1CCCC1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 1, 1, 1, 5, 8, 8, 8, 15, 16, 24, 24, 24, 24, 24, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 5, 5, 8, 15, 15, 24, 1, 1, 1, 1] 25
rigid atoms, others: [12, 13, 14, 51, 52, 53, 54, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 93
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: REAL300025051160 none CC(C)[N@@H+]1CCCC1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 6, 8, 13, 13, 13, 19, 20, 25, 25, 25, 25, 25, 6, 6, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 8, 8, 13, 19, 19, 25, 6, 6, 6, 6] 25
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 39, 40, 35, 41, 36, 38, 37] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 94
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051160 none CC(C)[N@@H+]1CCCC1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 25, 25, 24, 24, 24, 24, 24, 20, 20, 13, 20, 10, 1, 1, 1, 1, 1, 1, 1, 24, 24, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 24, 24, 24, 20, 13, 13, 1, 24, 24, 24, 24] 25
rigid atoms, others: [50, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54])
total number of confs: 77
number of broken/clashed sets: 25
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051160 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051160/1 /scratch/stefan/7786831/working/building/REAL300025051160 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 13)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/13
`/scratch/stefan/7786831/working/3D/13' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)[N@H+]1CCCC1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051160.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051160.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051160/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051160 none CC(C)[N@H+]1CCCC1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 4, 6, 6, 6, 9, 10, 13, 13, 13, 13, 13, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 6, 9, 9, 13, 1, 1, 1, 1] 14
rigid atoms, others: [12, 13, 14, 51, 52, 53, 54, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 54
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051160 none CC(C)[N@H+]1CCCC1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 3, 4, 4, 4, 4, 5, 8, 8, 8, 10, 11, 14, 14, 14, 14, 14, 4, 4, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 5, 5, 8, 10, 10, 14, 4, 4, 4, 4] 14
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 39, 40, 35, 41, 36, 38, 37] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 55
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051160 none CC(C)[N@H+]1CCCC1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 13, 13, 13, 13, 13, 13, 13, 10, 13, 8, 1, 1, 1, 1, 1, 1, 1, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 13, 13, 13, 13, 10, 10, 1, 13, 13, 13, 13] 14
rigid atoms, others: [50, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54])
total number of confs: 37
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051160 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051160
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051160/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051160/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051160
Building REAL300025051161
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051161'
/scratch/stefan/7786831/working/building/REAL300025051161 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051161

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051161/0 /scratch/stefan/7786831/working/building/REAL300025051161 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 14)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/14
`/scratch/stefan/7786831/working/3D/14' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CSC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051161.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051161.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051161/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051161 none O=C(CCC1=CSC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 5, 1, 1, 14, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 10, 12, 22, 22, 22, 22, 1, 1, 1, 6, 12, 12, 12, 32, 47, 105, 105, 105, 105, 105, 1, 1, 10, 10, 12, 12, 22, 22, 22, 2, 6, 6, 12, 32, 32, 105, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 304
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051161 none O=C(CCC1=CSC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 5, 1, 1, 14, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 7, 3, 1, 1, 1, 1, 1, 1, 22, 22, 22, 44, 57, 57, 57, 105, 135, 201, 201, 201, 201, 201, 22, 22, 7, 7, 3, 3, 1, 1, 1, 22, 44, 44, 57, 105, 105, 201, 22, 22, 22, 22] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 663
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051161 none O=C(CCC1=CSC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 5, 1, 1, 14, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [105, 105, 105, 150, 155, 201, 201, 201, 201, 105, 91, 47, 47, 25, 47, 13, 1, 1, 1, 1, 1, 1, 1, 105, 105, 150, 150, 155, 155, 201, 201, 201, 105, 91, 91, 47, 25, 25, 1, 105, 105, 105, 105] 201
rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 753
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051161 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051161
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051161/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051161
Building REAL300025051162
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051162'
/scratch/stefan/7786831/working/building/REAL300025051162 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051162

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051162/0 /scratch/stefan/7786831/working/building/REAL300025051162 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 15)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/15
`/scratch/stefan/7786831/working/3D/15' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC3=CC=CC=C3N=C2)CC1)

`REAL300025051162.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051162.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051162/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051162 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC3=CC=CC=C3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 31, 31, 106, 119, 200, 200, 200, 200, 200, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 106, 106, 200, 31, 6, 6, 3, 7, 7, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
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: REAL300025051162 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC3=CC=CC=C3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 30, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 146, 200, 200, 200, 200, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 30, 30, 1, 69, 146, 146, 200, 201, 201, 201, 201, 201, 200, 200, 200, 200] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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])
total number of confs: 729
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051162 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC3=CC=CC=C3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 48, 125, 132, 201, 201, 201, 201, 201, 12, 7, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 125, 125, 201, 48, 12, 12, 4, 1, 1, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43])
total number of confs: 596
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051162 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051162
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051162/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051162
Building REAL300025051163
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051163'
/scratch/stefan/7786831/working/building/REAL300025051163 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051163

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051163/0 /scratch/stefan/7786831/working/building/REAL300025051163 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 16)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/16
`/scratch/stefan/7786831/working/3D/16' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(F)C(F)=C2)CC1)

`REAL300025051163.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051163.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051163/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051163 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(F)C(F)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 59, 69, 109, 109, 109, 109, 109, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 1, 1, 59, 59, 109, 20, 5, 5, 3, 9, 9, 9, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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: REAL300025051163 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(F)C(F)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [54, 28, 13, 1, 1, 1, 1, 1, 1, 1, 54, 54, 88, 109, 109, 109, 109, 201, 201, 201, 201, 201, 201, 201, 109, 109, 28, 28, 1, 54, 88, 88, 109, 201, 201, 201, 109, 109, 109, 109] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 557
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051163 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(F)C(F)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 152, 169, 201, 201, 201, 201, 201, 17, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 152, 152, 201, 65, 17, 17, 5, 1, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [33, 34, 35, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39])
total number of confs: 692
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051163 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051163
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051163/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051163
Building REAL300025051164
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051164'
/scratch/stefan/7786831/working/building/REAL300025051164 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051164

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051164/0 /scratch/stefan/7786831/working/building/REAL300025051164 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 17)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/17
`/scratch/stefan/7786831/working/3D/17' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(F)=CC=C2F)CC1)

`REAL300025051164.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051164.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051164/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051164 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(F)=CC=C2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 15, 1, 1, 1, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 95, 108, 191, 191, 191, 191, 191, 6, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 1, 1, 95, 95, 191, 27, 6, 6, 3, 9, 5, 9, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 514
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051164 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(F)=CC=C2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 15, 1, 1, 1, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [73, 32, 13, 1, 1, 1, 1, 1, 1, 1, 73, 73, 142, 191, 191, 191, 191, 201, 201, 201, 201, 201, 201, 201, 191, 191, 32, 32, 1, 73, 142, 142, 191, 201, 201, 201, 191, 191, 191, 191] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 718
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051164 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(F)=CC=C2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 15, 1, 1, 1, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [56, 56, 56, 150, 158, 201, 201, 201, 201, 201, 16, 9, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 150, 150, 201, 56, 16, 16, 6, 1, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [33, 34, 35, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39])
total number of confs: 671
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051164 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051164
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051164/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051164
Building REAL300025051165
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051165'
/scratch/stefan/7786831/working/building/REAL300025051165 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051165

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051165/0 /scratch/stefan/7786831/working/building/REAL300025051165 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 18)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/18
`/scratch/stefan/7786831/working/3D/18' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(OCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1)

`REAL300025051165.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051165.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051165/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051165 none CC1=CC(OCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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: [22, 22, 22, 21, 10, 2, 2, 2, 1, 1, 1, 6, 15, 15, 15, 46, 65, 133, 133, 133, 133, 133, 1, 1, 22, 22, 22, 22, 22, 22, 10, 10, 2, 6, 6, 15, 46, 46, 133, 1, 1, 1, 1] 201
rigid atoms, others: [39, 8, 9, 10, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 354
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051165 none CC1=CC(OCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 3, 9, 22, 22, 22, 22, 34, 58, 58, 58, 113, 140, 201, 201, 201, 201, 201, 22, 22, 1, 1, 2, 2, 2, 1, 9, 9, 22, 34, 34, 58, 113, 113, 201, 22, 22, 22, 22] 201
rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 636
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051165 none CC1=CC(OCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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, 191, 133, 133, 133, 133, 114, 83, 83, 49, 83, 13, 1, 1, 1, 1, 1, 1, 1, 133, 133, 201, 201, 201, 201, 201, 201, 191, 191, 133, 114, 114, 83, 49, 49, 1, 133, 133, 133, 133] 201
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42])
total number of confs: 805
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051165 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051165
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051165/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051165
Building REAL300025051166
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051166'
/scratch/stefan/7786831/working/building/REAL300025051166 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051166

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051166/0 /scratch/stefan/7786831/working/building/REAL300025051166 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 19)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/19
`/scratch/stefan/7786831/working/3D/19' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1F)

`REAL300025051166.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051166.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051166/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051166 none COC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 14, 14, 14, 33, 37, 97, 97, 97, 97, 97, 1, 1, 5, 5, 5, 10, 10, 10, 5, 5, 2, 4, 4, 14, 33, 33, 97, 1, 1, 1, 1, 5] 201
rigid atoms, others: [39, 8, 9, 10, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 43])
total number of confs: 235
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051166 none COC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 5, 5, 5, 13, 37, 37, 37, 83, 91, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 3, 3, 3, 1, 1, 5, 13, 13, 37, 83, 83, 201, 5, 5, 5, 5, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 43, 24, 25, 26, 30, 31] set([0, 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])
total number of confs: 510
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051166 none COC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 97, 97, 97, 97, 78, 58, 58, 30, 58, 13, 1, 1, 1, 1, 1, 1, 1, 97, 97, 201, 201, 201, 201, 201, 201, 201, 201, 97, 78, 78, 58, 30, 30, 1, 97, 97, 97, 97, 201] 201
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42, 43])
total number of confs: 528
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051166 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051166
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051166/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051166
Building REAL300025051167
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051167'
/scratch/stefan/7786831/working/building/REAL300025051167 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051167

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051167/0 /scratch/stefan/7786831/working/building/REAL300025051167 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 20)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/20
`/scratch/stefan/7786831/working/3D/20' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(Cl)C=NC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051167.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051167.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051167/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051167 none CC1=C(Cl)C=NC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 16, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 37, 45, 113, 113, 113, 113, 113, 1, 1, 9, 9, 9, 9, 9, 2, 5, 5, 17, 37, 37, 113, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
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: REAL300025051167 none CC1=C(Cl)C=NC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 16, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 28, 63, 63, 63, 103, 115, 201, 201, 201, 201, 201, 9, 9, 2, 2, 2, 1, 1, 9, 28, 28, 63, 103, 103, 201, 9, 9, 9, 9] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 29, 30] set([9, 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])
total number of confs: 589
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051167 none CC1=C(Cl)C=NC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 16, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 113, 113, 113, 113, 75, 40, 40, 24, 40, 13, 1, 1, 1, 1, 1, 1, 1, 113, 113, 201, 201, 201, 201, 201, 113, 75, 75, 40, 24, 24, 1, 113, 113, 113, 113] 201
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41])
total number of confs: 556
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051167 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051167
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051167/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051167
Building REAL300025051168
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051168'
/scratch/stefan/7786831/working/building/REAL300025051168 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051168

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051168/0 /scratch/stefan/7786831/working/building/REAL300025051168 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 21)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/21
`/scratch/stefan/7786831/working/3D/21' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N(C)C=N1)

`REAL300025051168.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051168.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051168/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051168 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N(C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 2, 2, 2, 1, 1, 1, 4, 20, 20, 20, 89, 106, 162, 162, 162, 162, 162, 1, 1, 6, 6, 6, 6, 6, 6, 6, 2, 4, 4, 20, 89, 89, 162, 1, 1, 1, 1, 6, 6, 6, 6] 201
rigid atoms, others: [35, 36, 5, 6, 7, 19, 20, 38, 37] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42])
total number of confs: 451
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051168 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N(C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 6, 14, 51, 51, 51, 146, 164, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 14, 14, 51, 146, 146, 201, 6, 6, 6, 6, 2, 2, 2, 1] 201
rigid atoms, others: [0, 1, 2, 3, 42, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 659
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051168 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N(C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 162, 162, 162, 162, 132, 62, 62, 23, 62, 13, 1, 1, 1, 1, 1, 1, 1, 162, 162, 201, 201, 201, 201, 201, 201, 201, 162, 132, 132, 62, 23, 23, 1, 162, 162, 162, 162, 201, 201, 201, 201] 201
rigid atoms, others: [34, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 691
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051168 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051168
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051168/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051168
Building REAL300025051169
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051169'
/scratch/stefan/7786831/working/building/REAL300025051169 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051169

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051169/0 /scratch/stefan/7786831/working/building/REAL300025051169 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 22)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/22
`/scratch/stefan/7786831/working/3D/22' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(F)=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1F)

`REAL300025051169.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051169.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051169/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051169 none CC1=CC(F)=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 24, 24, 24, 74, 86, 190, 191, 191, 191, 191, 1, 1, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 24, 74, 74, 191, 1, 1, 1, 1, 4] 201
rigid atoms, others: [38, 39, 8, 9, 10, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 42])
total number of confs: 485
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051169 none CC1=CC(F)=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 17, 55, 55, 55, 128, 137, 200, 201, 201, 201, 201, 4, 4, 1, 1, 1, 2, 2, 2, 1, 4, 17, 17, 55, 128, 128, 201, 4, 4, 4, 4, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 24, 25, 26, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 633
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051169 none CC1=CC(F)=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 191, 191, 191, 191, 116, 48, 48, 29, 48, 13, 1, 1, 1, 1, 1, 1, 1, 191, 191, 201, 201, 201, 201, 201, 201, 201, 191, 116, 116, 48, 29, 29, 1, 191, 191, 191, 191, 201] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 739
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051169 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051169
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051169/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051169
Building REAL300025051170
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051170'
/scratch/stefan/7786831/working/building/REAL300025051170 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051170

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051170/0 /scratch/stefan/7786831/working/building/REAL300025051170 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 23)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/23
`/scratch/stefan/7786831/working/3D/23' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCC1=CSC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051170.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051170.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051170/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051170 none O=C(CCCC1=CSC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 14, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 10, 15, 21, 36, 36, 36, 36, 1, 1, 1, 4, 6, 6, 6, 18, 23, 59, 59, 59, 59, 59, 1, 1, 10, 10, 19, 19, 21, 21, 36, 36, 36, 2, 4, 4, 6, 18, 18, 59, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
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: REAL300025051170 none O=C(CCCC1=CSC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 14, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [35, 8, 4, 2, 1, 1, 1, 1, 1, 1, 35, 36, 36, 46, 60, 60, 60, 96, 122, 201, 201, 201, 201, 201, 36, 36, 8, 8, 4, 4, 2, 2, 1, 1, 1, 36, 46, 46, 60, 96, 96, 201, 36, 36, 36, 36] 201
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 624
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051170 none O=C(CCCC1=CSC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 14, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 114, 129, 138, 201, 201, 201, 201, 59, 54, 34, 34, 22, 34, 12, 1, 1, 1, 1, 1, 1, 1, 59, 59, 114, 114, 136, 136, 138, 138, 201, 201, 201, 59, 54, 54, 34, 22, 22, 1, 59, 59, 59, 59] 201
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 760
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051170 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051170
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051170/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051170
Building REAL300025051171
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051171'
/scratch/stefan/7786831/working/building/REAL300025051171 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051171

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051171/0 /scratch/stefan/7786831/working/building/REAL300025051171 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 24)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/24
`/scratch/stefan/7786831/working/3D/24' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3C=CNC3=N2)CC1)

`REAL300025051171.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051171.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051171/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051171 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3C=CNC3=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 31, 31, 105, 117, 196, 196, 196, 196, 196, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 105, 105, 196, 31, 6, 6, 3, 7, 7, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 543
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051171 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3C=CNC3=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 33, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 153, 196, 196, 196, 196, 201, 201, 201, 201, 201, 201, 201, 201, 196, 196, 33, 33, 1, 77, 153, 153, 196, 201, 201, 201, 201, 201, 196, 196, 196, 196] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 739
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051171 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3C=CNC3=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [50, 50, 50, 129, 137, 201, 201, 201, 201, 201, 12, 7, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 129, 129, 201, 50, 12, 12, 4, 1, 1, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42])
total number of confs: 609
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051171 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051171
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051171/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051171
Building REAL300025051172
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051172'
/scratch/stefan/7786831/working/building/REAL300025051172 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051172

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051172/0 /scratch/stefan/7786831/working/building/REAL300025051172 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 25)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/25
`/scratch/stefan/7786831/working/3D/25' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3NC=CC3=C2)CC1)

`REAL300025051172.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051172.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051172/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051172 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3NC=CC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 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: [25, 25, 25, 74, 85, 136, 136, 136, 136, 136, 6, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 74, 74, 136, 25, 6, 6, 3, 9, 9, 9, 9, 9, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 385
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051172 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3NC=CC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 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: [66, 30, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 110, 136, 136, 136, 136, 201, 201, 201, 201, 201, 201, 201, 201, 136, 136, 30, 30, 1, 66, 110, 110, 136, 201, 201, 201, 201, 201, 136, 136, 136, 136] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 615
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051172 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3NC=CC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 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: [61, 61, 61, 153, 167, 201, 201, 201, 201, 201, 15, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 153, 153, 201, 61, 15, 15, 5, 1, 1, 1, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42])
total number of confs: 670
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051172 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051172
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051172/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051172
Building REAL300025051173
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051173'
/scratch/stefan/7786831/working/building/REAL300025051173 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051173

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051173/0 /scratch/stefan/7786831/working/building/REAL300025051173 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 26)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/26
`/scratch/stefan/7786831/working/3D/26' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CN=CS2)CC1)

`REAL300025051173.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051173.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051173/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051173 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CN=CS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 14, 14, 36, 44, 109, 109, 109, 109, 109, 5, 1, 1, 1, 3, 3, 3, 20, 35, 35, 35, 35, 1, 1, 36, 36, 109, 14, 5, 5, 3, 20, 20, 35, 35, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
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: REAL300025051173 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CN=CS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [55, 28, 13, 1, 1, 1, 1, 1, 1, 1, 55, 55, 92, 109, 109, 109, 109, 177, 201, 201, 201, 201, 109, 109, 28, 28, 1, 55, 92, 92, 109, 177, 177, 201, 201, 109, 109, 109, 109] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 782
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051173 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CN=CS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [92, 92, 92, 153, 166, 201, 201, 201, 201, 201, 48, 35, 24, 23, 4, 23, 1, 1, 1, 1, 1, 1, 35, 35, 153, 153, 201, 92, 48, 48, 24, 4, 4, 1, 1, 35, 35, 35, 35] 201
rigid atoms, others: [33, 34, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38])
total number of confs: 697
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051173 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051173
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051173/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051173
Building REAL300025051174
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051174'
/scratch/stefan/7786831/working/building/REAL300025051174 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051174

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051174/0 /scratch/stefan/7786831/working/building/REAL300025051174 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 27)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/27
`/scratch/stefan/7786831/working/3D/27' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(=O)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CN1C)

`REAL300025051174.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051174.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051174/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051174 none CC1=CC(=O)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 7, 29, 29, 29, 85, 110, 198, 198, 198, 198, 198, 1, 1, 5, 5, 5, 5, 5, 5, 5, 2, 7, 7, 29, 85, 85, 198, 1, 1, 1, 1, 5, 5, 5, 5] 201
rigid atoms, others: [38, 39, 8, 9, 10, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 42, 43, 44, 45])
total number of confs: 517
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051174 none CC1=CC(=O)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 15, 44, 44, 44, 108, 129, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 44, 108, 108, 201, 5, 5, 5, 5, 1, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45])
total number of confs: 583
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051174 none CC1=CC(=O)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 198, 198, 198, 198, 135, 68, 68, 28, 68, 13, 1, 1, 1, 1, 1, 1, 1, 198, 198, 201, 201, 201, 201, 201, 201, 201, 198, 135, 135, 68, 28, 28, 1, 198, 198, 198, 198, 201, 201, 201, 201] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 716
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051174 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051174
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051174/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051174
Building REAL300025051175
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051175'
/scratch/stefan/7786831/working/building/REAL300025051175 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051175

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051175/0 /scratch/stefan/7786831/working/building/REAL300025051175 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 28)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/28
`/scratch/stefan/7786831/working/3D/28' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(=O)NN=C2)CC1)

`REAL300025051175.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051175.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051175/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051175 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(=O)NN=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 25, 71, 81, 137, 137, 137, 137, 137, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 1, 1, 71, 71, 137, 25, 5, 5, 3, 9, 9, 9, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
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: REAL300025051175 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(=O)NN=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [57, 27, 12, 1, 1, 1, 1, 1, 1, 1, 57, 57, 100, 137, 137, 137, 137, 201, 201, 201, 201, 201, 201, 137, 137, 27, 27, 1, 57, 100, 100, 137, 201, 201, 201, 137, 137, 137, 137] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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])
total number of confs: 611
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051175 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(=O)NN=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [64, 64, 64, 140, 152, 201, 201, 201, 201, 201, 16, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 9, 9, 140, 140, 201, 64, 16, 16, 5, 1, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38])
total number of confs: 658
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051175 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051175
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051175/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051175
Building REAL300025051176
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051176'
/scratch/stefan/7786831/working/building/REAL300025051176 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051176

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051176/0 /scratch/stefan/7786831/working/building/REAL300025051176 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 29)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/29
`/scratch/stefan/7786831/working/3D/29' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)NC(=O)N1)

`REAL300025051176.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051176.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051176/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051176 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)NC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', '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, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 2, 2, 2, 1, 1, 1, 4, 20, 20, 20, 53, 64, 103, 103, 103, 103, 103, 1, 1, 9, 9, 9, 9, 9, 9, 9, 2, 4, 4, 20, 53, 53, 103, 1, 1, 1, 1, 9, 9] 141
rigid atoms, others: [35, 36, 5, 6, 7, 19, 20, 38, 37] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40])
total number of confs: 294
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051176 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)NC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', '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, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 9, 9, 9, 9, 17, 54, 54, 54, 98, 112, 141, 141, 141, 141, 141, 9, 9, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 54, 98, 98, 141, 9, 9, 9, 9, 1, 1] 141
rigid atoms, others: [0, 1, 2, 3, 39, 40, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 466
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051176 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)NC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', '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, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [141, 141, 103, 103, 103, 103, 81, 54, 54, 27, 54, 13, 1, 1, 1, 1, 1, 1, 1, 103, 103, 141, 141, 141, 141, 141, 141, 141, 103, 81, 81, 54, 27, 27, 1, 103, 103, 103, 103, 141, 141] 141
rigid atoms, others: [34, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40])
total number of confs: 442
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051176 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051176
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051176/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051176
Building REAL300025051177
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051177'
/scratch/stefan/7786831/working/building/REAL300025051177 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051177

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051177/0 /scratch/stefan/7786831/working/building/REAL300025051177 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 30)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/30
`/scratch/stefan/7786831/working/3D/30' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CSC=C2Cl)CC1)

`REAL300025051177.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051177.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051177/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051177 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CSC=C2Cl)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 16, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 25, 71, 86, 158, 158, 158, 158, 158, 5, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 1, 1, 71, 71, 158, 25, 5, 5, 3, 10, 10, 1, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 411
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051177 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CSC=C2Cl)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 16, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [65, 29, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 126, 158, 158, 158, 158, 201, 201, 201, 201, 201, 158, 158, 29, 29, 1, 65, 126, 126, 158, 201, 201, 158, 158, 158, 158] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 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])
total number of confs: 647
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051177 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CSC=C2Cl)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 16, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [56, 56, 56, 130, 145, 201, 201, 201, 201, 201, 16, 10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 130, 130, 201, 56, 16, 16, 6, 1, 1, 10, 10, 10, 10] 201
rigid atoms, others: [32, 14, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36])
total number of confs: 629
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051177 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051177
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051177/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051177
Building REAL300025051178
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051178'
/scratch/stefan/7786831/working/building/REAL300025051178 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051178

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051178/0 /scratch/stefan/7786831/working/building/REAL300025051178 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 31)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/31
`/scratch/stefan/7786831/working/3D/31' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=NN(C)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051178.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051178.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051178/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051178 none CCC1=NN(C)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 6, 6, 6, 6, 2, 2, 2, 1, 1, 1, 4, 10, 10, 10, 26, 40, 113, 113, 113, 113, 113, 1, 1, 15, 15, 15, 15, 15, 6, 6, 6, 6, 2, 4, 4, 10, 26, 26, 113, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 278
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051178 none CCC1=NN(C)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 12, 24, 24, 24, 56, 81, 145, 145, 145, 145, 145, 6, 6, 6, 6, 6, 5, 5, 2, 2, 2, 1, 6, 12, 12, 24, 56, 56, 145, 6, 6, 6, 6] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 34] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 409
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051178 none CCC1=NN(C)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 145, 145, 145, 145, 145, 145, 113, 113, 113, 113, 94, 50, 50, 21, 50, 11, 1, 1, 1, 1, 1, 1, 1, 113, 113, 201, 201, 201, 201, 201, 145, 145, 145, 145, 113, 94, 94, 50, 21, 21, 1, 113, 113, 113, 113] 201
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 851
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051178 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051178
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051178/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051178
Building REAL300025051179
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051179'
/scratch/stefan/7786831/working/building/REAL300025051179 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051179

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051179/0 /scratch/stefan/7786831/working/building/REAL300025051179 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 32)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/32
`/scratch/stefan/7786831/working/3D/32' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025051179.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051179.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051179/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051179 none COC1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 9, 9, 9, 2, 2, 2, 1, 1, 1, 4, 9, 9, 9, 27, 46, 153, 153, 153, 153, 153, 1, 1, 9, 16, 16, 16, 9, 9, 9, 9, 2, 4, 4, 9, 27, 27, 153, 1, 1, 1, 1, 9, 9] 201
rigid atoms, others: [38, 7, 8, 9, 39, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 42, 43])
total number of confs: 312
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051179 none COC1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 9, 9, 9, 9, 22, 34, 34, 34, 84, 115, 201, 201, 201, 201, 201, 9, 9, 1, 4, 4, 4, 1, 1, 1, 1, 9, 22, 22, 34, 84, 84, 201, 9, 9, 9, 9, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 42, 43, 23, 27, 28, 29, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 559
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051179 none COC1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 153, 153, 153, 153, 130, 75, 75, 30, 75, 13, 1, 1, 1, 1, 1, 1, 1, 153, 153, 201, 201, 201, 201, 201, 201, 201, 201, 153, 130, 130, 75, 30, 30, 1, 153, 153, 153, 153, 201, 201] 201
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43])
total number of confs: 807
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051179 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051179
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051179/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051179
Building REAL300025051180
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051180'
/scratch/stefan/7786831/working/building/REAL300025051180 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051180

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051180/0 /scratch/stefan/7786831/working/building/REAL300025051180 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 33)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/33
`/scratch/stefan/7786831/working/3D/33' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@H]2CCCC(=O)N2)CC1)

`REAL300025051180.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051180.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051180/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051180 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@H]2CCCC(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 25, 76, 89, 167, 167, 167, 167, 167, 6, 1, 1, 1, 3, 3, 3, 18, 18, 18, 18, 18, 18, 18, 1, 1, 76, 76, 167, 25, 6, 6, 3, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 457
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051180 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@H]2CCCC(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [84, 39, 12, 1, 1, 1, 1, 1, 1, 1, 84, 84, 139, 167, 167, 167, 167, 201, 201, 201, 201, 201, 201, 201, 167, 167, 39, 39, 1, 84, 139, 139, 167, 201, 201, 201, 201, 201, 201, 201, 167, 167, 167, 167] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 739
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051180 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@H]2CCCC(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [71, 71, 71, 146, 157, 201, 201, 201, 201, 201, 28, 18, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 146, 146, 201, 71, 28, 28, 10, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43])
total number of confs: 680
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051180 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051180
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051180/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051180
Building REAL300025051181
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051181'
/scratch/stefan/7786831/working/building/REAL300025051181 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051181

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051181/0 /scratch/stefan/7786831/working/building/REAL300025051181 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 34)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/34
`/scratch/stefan/7786831/working/3D/34' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CN=C1COCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051181.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051181.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051181/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051181 none CN1C=CN=C1COCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 26, 26, 26, 26, 22, 17, 6, 2, 2, 2, 1, 1, 1, 5, 13, 13, 13, 42, 60, 119, 119, 119, 119, 119, 1, 1, 26, 26, 26, 26, 26, 22, 22, 6, 6, 2, 5, 5, 13, 42, 42, 119, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
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: REAL300025051181 none CN1C=CN=C1COCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 11, 16, 26, 26, 26, 26, 42, 57, 57, 57, 118, 148, 201, 201, 201, 201, 201, 26, 26, 2, 2, 2, 1, 1, 6, 6, 16, 16, 26, 42, 42, 57, 118, 118, 201, 26, 26, 26, 26] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 662
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051181 none CN1C=CN=C1COCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 200, 196, 165, 119, 119, 119, 119, 102, 71, 71, 46, 71, 13, 1, 1, 1, 1, 1, 1, 1, 119, 119, 201, 201, 201, 201, 201, 200, 200, 165, 165, 119, 102, 102, 71, 46, 46, 1, 119, 119, 119, 119] 201
rigid atoms, others: [42, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46])
total number of confs: 781
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051181 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051181
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051181/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051181
Building REAL300025051182
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051182'
/scratch/stefan/7786831/working/building/REAL300025051182 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051182

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051182/0 /scratch/stefan/7786831/working/building/REAL300025051182 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 35)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/35
`/scratch/stefan/7786831/working/3D/35' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CCC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1=O)

`REAL300025051182.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051182.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051182/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051182 none CN1CCC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 5, 2, 2, 2, 1, 1, 1, 7, 21, 21, 21, 64, 84, 177, 177, 177, 177, 177, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 2, 7, 7, 21, 64, 64, 177, 1, 1, 1, 1] 201
rigid atoms, others: [8, 9, 10, 43, 44, 45, 46, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
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: REAL300025051182 none CN1CCC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations 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, 11, 11, 11, 11, 23, 52, 52, 52, 106, 129, 201, 201, 201, 201, 201, 11, 11, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 5, 5, 11, 23, 23, 52, 106, 106, 201, 11, 11, 11, 11] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 24, 25, 33, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 628
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051182 none CN1CCC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 193, 177, 177, 177, 177, 130, 66, 66, 29, 66, 13, 1, 1, 1, 1, 1, 1, 1, 177, 177, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 193, 193, 177, 130, 130, 66, 29, 29, 1, 177, 177, 177, 177] 201
rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46])
total number of confs: 796
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051182 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051182
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051182/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051182
Building REAL300025051183
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051183'
/scratch/stefan/7786831/working/building/REAL300025051183 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051183

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051183/0 /scratch/stefan/7786831/working/building/REAL300025051183 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 36)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/36
`/scratch/stefan/7786831/working/3D/36' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NN3CCCCC3=C2)CC1)

`REAL300025051183.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051183.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051183/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051183 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NN3CCCCC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 8, 5, 5, 5, 5, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 31, 31, 109, 118, 201, 201, 201, 201, 201, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 109, 109, 201, 31, 6, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 569
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051183 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NN3CCCCC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 8, 5, 5, 5, 5, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [62, 31, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 154, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 31, 31, 1, 62, 154, 154, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46])
total number of confs: 751
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051183 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NN3CCCCC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 8, 5, 5, 5, 5, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [43, 43, 43, 122, 129, 201, 201, 201, 201, 201, 11, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 122, 122, 201, 43, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46])
total number of confs: 591
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051183 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051183
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051183/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051183
Building REAL300025051184
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051184'
/scratch/stefan/7786831/working/building/REAL300025051184 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051184

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051184/0 /scratch/stefan/7786831/working/building/REAL300025051184 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 37)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/37
`/scratch/stefan/7786831/working/3D/37' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC[N@H+](CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025051184.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051184.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051184/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051184 none CC1CC[N@H+](CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 9, 6, 9, 2, 2, 2, 1, 1, 1, 4, 7, 7, 7, 16, 20, 28, 28, 28, 28, 28, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 2, 4, 4, 7, 16, 16, 28, 1, 1, 1, 1, 9, 9] 32
rigid atoms, others: [43, 9, 10, 11, 44, 45, 46, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48])
total number of confs: 116
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051184 none CC1CC[N@H+](CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 9, 11, 15, 15, 15, 23, 26, 32, 32, 32, 32, 32, 9, 9, 1, 2, 2, 2, 1, 1, 1, 1, 1, 4, 4, 9, 11, 11, 15, 23, 23, 32, 9, 9, 9, 9, 1, 1] 32
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 47, 48, 25, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 118
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051184 none CC1CC[N@H+](CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [32, 32, 32, 32, 32, 32, 28, 28, 28, 28, 25, 22, 22, 16, 22, 10, 1, 1, 1, 1, 1, 1, 1, 28, 28, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 28, 25, 25, 22, 16, 16, 1, 28, 28, 28, 28, 32, 32] 32
rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48])
total number of confs: 119
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051184 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051184/1 /scratch/stefan/7786831/working/building/REAL300025051184 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 38)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/38
`/scratch/stefan/7786831/working/3D/38' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC[N@@H+](CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025051184.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051184.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051184/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051184 none CC1CC[N@@H+](CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 9, 5, 9, 2, 2, 2, 1, 1, 1, 4, 7, 7, 7, 17, 23, 36, 36, 36, 36, 36, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 2, 4, 4, 7, 17, 17, 36, 1, 1, 1, 1, 9, 9] 39
rigid atoms, others: [43, 9, 10, 11, 44, 45, 46, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48])
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: REAL300025051184 none CC1CC[N@@H+](CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 4, 9, 9, 9, 9, 11, 17, 17, 17, 25, 28, 39, 39, 39, 39, 39, 9, 9, 1, 2, 2, 2, 1, 1, 1, 1, 1, 4, 4, 9, 11, 11, 17, 25, 25, 39, 9, 9, 9, 9, 1, 1] 39
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 47, 48, 25, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 132
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051184 none CC1CC[N@@H+](CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 36, 36, 36, 36, 34, 29, 29, 20, 29, 11, 1, 1, 1, 1, 1, 1, 1, 36, 36, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 36, 34, 34, 29, 20, 20, 1, 36, 36, 36, 36, 39, 39] 39
rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48])
total number of confs: 145
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051184 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051184
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051184/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051184/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051184
Building REAL300025051185
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051185'
/scratch/stefan/7786831/working/building/REAL300025051185 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051185

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051185/0 /scratch/stefan/7786831/working/building/REAL300025051185 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 39)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/39
`/scratch/stefan/7786831/working/3D/39' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3=CC=NC=C3C2)CC1)

`REAL300025051185.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051185.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051185/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051185 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3=CC=NC=C3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 1, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 49, 60, 133, 133, 133, 133, 133, 5, 1, 1, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 49, 49, 133, 16, 5, 5, 3, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 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: REAL300025051185 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3=CC=NC=C3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 1, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 31, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 114, 133, 133, 133, 133, 201, 201, 201, 201, 201, 201, 201, 201, 133, 133, 31, 31, 1, 65, 114, 114, 133, 201, 201, 201, 201, 201, 201, 201, 201, 133, 133, 133, 133] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45])
total number of confs: 732
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051185 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3=CC=NC=C3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 1, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 143, 157, 201, 201, 201, 201, 201, 23, 17, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 143, 143, 201, 66, 23, 23, 9, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44, 45])
total number of confs: 672
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051185 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051185
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051185/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051185
Building REAL300025051186
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051186'
/scratch/stefan/7786831/working/building/REAL300025051186 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051186

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051186/0 /scratch/stefan/7786831/working/building/REAL300025051186 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 40)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/40
`/scratch/stefan/7786831/working/3D/40' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC(F)(F)C(F)F)CC1)

`REAL300025051186.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051186.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051186/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051186 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC(F)(F)C(F)F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 15, 15, 5, 15, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 12, 24, 28, 48, 48, 48, 48, 48, 4, 1, 1, 1, 3, 3, 3, 18, 64, 64, 56, 80, 79, 1, 1, 24, 24, 48, 12, 4, 4, 3, 18, 18, 72, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 474
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051186 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC(F)(F)C(F)F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 15, 15, 5, 15, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [33, 17, 11, 1, 1, 1, 1, 1, 1, 1, 33, 33, 45, 48, 48, 48, 48, 136, 200, 200, 184, 201, 201, 48, 48, 17, 17, 1, 33, 45, 45, 48, 136, 136, 185, 48, 48, 48, 48] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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])
total number of confs: 956
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051186 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051186
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051186/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051186
Building REAL300025051187
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051187'
/scratch/stefan/7786831/working/building/REAL300025051187 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051187

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051187/0 /scratch/stefan/7786831/working/building/REAL300025051187 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 41)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/41
`/scratch/stefan/7786831/working/3D/41' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC[N@H+](CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025051187.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051187.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051187/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051187 none CC1(C)CC[N@H+](CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 9, 9, 5, 9, 2, 2, 2, 1, 1, 1, 3, 5, 5, 5, 12, 16, 34, 34, 34, 34, 34, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 2, 3, 3, 5, 12, 12, 34, 1, 1, 1, 1, 9, 9] 35
rigid atoms, others: [10, 11, 12, 46, 47, 48, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51])
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: REAL300025051187 none CC1(C)CC[N@H+](CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 4, 9, 9, 9, 9, 10, 15, 15, 15, 23, 25, 35, 35, 35, 35, 35, 9, 9, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 9, 10, 10, 15, 23, 23, 35, 9, 9, 9, 9, 1, 1] 35
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 7, 34, 50, 35, 36, 26, 51] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 125
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051187 none CC1(C)CC[N@H+](CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 34, 34, 34, 34, 34, 30, 30, 18, 30, 10, 1, 1, 1, 1, 1, 1, 1, 34, 34, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 34, 34, 34, 30, 18, 18, 1, 34, 34, 34, 34, 35, 35] 35
rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51])
total number of confs: 121
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051187 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051187/1 /scratch/stefan/7786831/working/building/REAL300025051187 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 42)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/42
`/scratch/stefan/7786831/working/3D/42' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC[N@@H+](CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025051187.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051187.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051187/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051187 none CC1(C)CC[N@@H+](CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [16, 16, 16, 16, 16, 7, 16, 2, 2, 2, 1, 1, 1, 5, 14, 14, 14, 33, 48, 90, 90, 90, 90, 90, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 7, 2, 5, 5, 14, 33, 33, 90, 1, 1, 1, 1, 16, 16] 101
rigid atoms, others: [10, 11, 12, 46, 47, 48, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51])
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: REAL300025051187 none CC1(C)CC[N@@H+](CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 21, 38, 38, 38, 59, 73, 101, 101, 101, 101, 101, 16, 16, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 5, 5, 16, 21, 21, 38, 59, 59, 101, 16, 16, 16, 16, 1, 1] 101
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 7, 34, 50, 35, 36, 26, 51] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 323
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051187 none CC1(C)CC[N@@H+](CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [101, 101, 101, 101, 101, 99, 101, 90, 90, 90, 90, 80, 61, 61, 25, 61, 12, 1, 1, 1, 1, 1, 1, 1, 90, 90, 101, 101, 101, 101, 101, 101, 101, 101, 101, 101, 101, 99, 99, 90, 80, 80, 61, 25, 25, 1, 90, 90, 90, 90, 101, 101] 101
rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51])
total number of confs: 400
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051187 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051187
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051187/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051187/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051187
Building REAL300025051188
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051188'
/scratch/stefan/7786831/working/building/REAL300025051188 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051188

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051188/0 /scratch/stefan/7786831/working/building/REAL300025051188 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 43)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/43
`/scratch/stefan/7786831/working/3D/43' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@H+](CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)CC(C)(C)C)

`REAL300025051188.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051188.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051188/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051188 none C[N@H+](CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)CC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 32, 22, 22, 16, 22, 12, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 32, 32, 22, 16, 16, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 35
rigid atoms, others: [38, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 125
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: REAL300025051188 none C[N@H+](CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)CC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 8, 2, 2, 2, 1, 1, 1, 5, 11, 11, 11, 18, 22, 35, 35, 35, 35, 35, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 2, 5, 5, 11, 18, 18, 35, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 35
rigid atoms, others: [6, 39, 8, 41, 42, 7, 40, 20, 21] set([0, 1, 2, 3, 4, 5, 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, 36, 37, 38, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 131
number of broken/clashed sets: 35
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051188 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051188/1 /scratch/stefan/7786831/working/building/REAL300025051188 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 44)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/44
`/scratch/stefan/7786831/working/3D/44' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@@H+](CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)CC(C)(C)C)

`REAL300025051188.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051188.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051188/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051188 none C[N@@H+](CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)CC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 17, 17, 17, 17, 15, 13, 13, 11, 13, 9, 1, 1, 1, 1, 1, 1, 1, 17, 17, 21, 21, 21, 21, 21, 21, 21, 21, 20, 20, 17, 15, 15, 13, 11, 11, 1, 17, 17, 17, 17, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 21
rigid atoms, others: [38, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 74
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: REAL300025051188 none C[N@@H+](CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)CC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [5, 3, 5, 2, 2, 2, 1, 1, 1, 3, 4, 4, 4, 7, 9, 17, 17, 17, 17, 17, 1, 1, 5, 6, 6, 6, 6, 5, 5, 5, 3, 3, 2, 3, 3, 4, 7, 7, 17, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 21
rigid atoms, others: [6, 39, 8, 41, 42, 7, 40, 20, 21] set([0, 1, 2, 3, 4, 5, 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, 36, 37, 38, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 73
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051188 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051188
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051188/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051188/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051188
Building REAL300025051189
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051189'
/scratch/stefan/7786831/working/building/REAL300025051189 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051189

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051189/0 /scratch/stefan/7786831/working/building/REAL300025051189 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 45)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/45
`/scratch/stefan/7786831/working/3D/45' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CN=CS1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051189.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051189.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051189/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051189 none O=C(CCC1=CN=CS1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 14, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 10, 14, 22, 22, 22, 22, 1, 1, 1, 6, 13, 13, 13, 38, 56, 118, 118, 118, 118, 118, 1, 1, 10, 10, 14, 14, 22, 22, 2, 6, 6, 13, 38, 38, 118, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 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: REAL300025051189 none O=C(CCC1=CN=CS1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 14, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 4, 2, 1, 1, 1, 1, 1, 1, 22, 22, 22, 45, 58, 58, 58, 98, 131, 201, 201, 201, 201, 201, 22, 22, 4, 4, 2, 2, 1, 1, 22, 45, 45, 58, 98, 98, 201, 22, 22, 22, 22] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 29, 30] set([0, 1, 2, 9, 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])
total number of confs: 620
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051189 none O=C(CCC1=CN=CS1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 14, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [118, 118, 118, 180, 185, 201, 201, 201, 201, 118, 110, 68, 68, 30, 68, 13, 1, 1, 1, 1, 1, 1, 1, 118, 118, 180, 180, 185, 185, 201, 201, 118, 110, 110, 68, 30, 30, 1, 118, 118, 118, 118] 201
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41])
total number of confs: 791
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051189 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051189
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051189/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051189
Building REAL300025051190
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051190'
/scratch/stefan/7786831/working/building/REAL300025051190 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051190

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051190/0 /scratch/stefan/7786831/working/building/REAL300025051190 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 46)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/46
`/scratch/stefan/7786831/working/3D/46' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)[C@@H]1CC[C@H](C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025051190.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051190.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051190/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051190 none NC(=O)[C@@H]1CC[C@H](C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 6, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 9, 20, 9, 9, 9, 9, 2, 9, 2, 2, 1, 1, 1, 4, 6, 6, 6, 24, 44, 134, 134, 134, 134, 134, 1, 1, 9, 20, 20, 9, 9, 9, 9, 2, 4, 4, 6, 24, 24, 134, 1, 1, 1, 1, 9, 9] 201
rigid atoms, others: [43, 41, 42, 11, 12, 13, 44, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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, 45, 46])
total number of confs: 304
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051190 none NC(=O)[C@@H]1CC[C@H](C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 6, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 16, 26, 26, 26, 79, 112, 196, 196, 196, 196, 196, 9, 9, 1, 8, 8, 1, 1, 1, 1, 9, 16, 16, 26, 79, 79, 196, 9, 9, 9, 9, 1, 1] 201
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 45, 46, 33, 27, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 553
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051190 none NC(=O)[C@@H]1CC[C@H](C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 6, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 196, 201, 196, 196, 196, 196, 134, 196, 134, 134, 134, 114, 72, 72, 31, 72, 12, 1, 1, 1, 1, 1, 1, 1, 134, 134, 196, 201, 201, 196, 196, 196, 196, 134, 114, 114, 72, 31, 31, 1, 134, 134, 134, 134, 196, 196] 201
rigid atoms, others: [40, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46])
total number of confs: 744
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051190 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051190
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051190/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051190
Building REAL300025051191
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051191'
/scratch/stefan/7786831/working/building/REAL300025051191 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051191

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051191/0 /scratch/stefan/7786831/working/building/REAL300025051191 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 47)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/47
`/scratch/stefan/7786831/working/3D/47' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)[C@@H]1C[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051191.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051191.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051191/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051191 none NC(=O)[C@@H]1C[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 7, 10, 7, 7, 7, 2, 7, 2, 2, 1, 1, 1, 7, 17, 17, 17, 59, 86, 176, 176, 176, 176, 176, 1, 1, 10, 10, 7, 7, 2, 7, 7, 17, 59, 59, 176, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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: REAL300025051191 none NC(=O)[C@@H]1C[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 20, 36, 36, 36, 103, 135, 201, 201, 201, 201, 201, 7, 7, 5, 5, 1, 1, 7, 20, 20, 36, 103, 103, 201, 7, 7, 7, 7] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 28, 29] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 614
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051191 none NC(=O)[C@@H]1C[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 176, 201, 176, 176, 176, 149, 77, 77, 29, 77, 12, 1, 1, 1, 1, 1, 1, 1, 176, 176, 201, 201, 201, 201, 176, 149, 149, 77, 29, 29, 1, 176, 176, 176, 176] 201
rigid atoms, others: [36, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 756
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051191 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051191
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051191/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051191
Building REAL300025051192
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051192'
/scratch/stefan/7786831/working/building/REAL300025051192 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051192

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051192/0 /scratch/stefan/7786831/working/building/REAL300025051192 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 48)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/48
`/scratch/stefan/7786831/working/3D/48' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C(C(F)F)N=CO2)CC1)

`REAL300025051192.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051192.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051192/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051192 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C(C(F)F)N=CO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 15, 15, 8, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 9, 9, 20, 23, 50, 50, 50, 50, 50, 4, 1, 1, 1, 3, 3, 3, 13, 13, 28, 28, 13, 13, 13, 1, 1, 20, 20, 50, 9, 4, 4, 3, 28, 13, 1, 1, 1, 1] 112
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 208
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051192 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C(C(F)F)N=CO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 15, 15, 8, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [35, 18, 11, 1, 1, 1, 1, 1, 1, 1, 35, 35, 50, 50, 50, 50, 50, 101, 101, 113, 113, 101, 101, 101, 50, 50, 18, 18, 1, 35, 50, 50, 50, 113, 101, 50, 50, 50, 50] 113
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 354
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051192 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C(C(F)F)N=CO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 15, 15, 8, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 29, 29, 56, 62, 101, 101, 101, 101, 101, 16, 13, 8, 8, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 13, 13, 56, 56, 101, 29, 16, 16, 8, 8, 1, 13, 13, 13, 13] 112
rigid atoms, others: [34, 14, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 338
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051192 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051192
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051192/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051192
Building REAL300025051193
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051193'
/scratch/stefan/7786831/working/building/REAL300025051193 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051193

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051193/0 /scratch/stefan/7786831/working/building/REAL300025051193 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 49)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/49
`/scratch/stefan/7786831/working/3D/49' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1)

`REAL300025051193.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051193.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051193/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051193 none CN1N=CC(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 25, 25, 14, 9, 2, 2, 2, 1, 1, 1, 6, 9, 9, 9, 32, 54, 122, 122, 122, 122, 122, 1, 1, 25, 25, 25, 25, 25, 14, 14, 9, 9, 2, 6, 6, 9, 32, 32, 122, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
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: REAL300025051193 none CN1N=CC(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 10, 25, 25, 25, 25, 36, 54, 54, 54, 100, 136, 201, 201, 201, 201, 201, 25, 25, 1, 2, 2, 2, 1, 6, 6, 10, 10, 25, 36, 36, 54, 100, 100, 201, 25, 25, 25, 25] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 29] set([6, 7, 8, 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: 637
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051193 none CN1N=CC(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 198, 122, 122, 122, 122, 111, 78, 78, 31, 78, 13, 1, 1, 1, 1, 1, 1, 1, 122, 122, 201, 201, 201, 201, 201, 201, 201, 198, 198, 122, 111, 111, 78, 31, 31, 1, 122, 122, 122, 122] 201
rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 821
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051193 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051193
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051193/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051193
Building REAL300025051194
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051194'
/scratch/stefan/7786831/working/building/REAL300025051194 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051194

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051194/0 /scratch/stefan/7786831/working/building/REAL300025051194 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 50)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/50
`/scratch/stefan/7786831/working/3D/50' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N1)

`REAL300025051194.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051194.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051194/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051194 none NC(=O)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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: [7, 5, 7, 5, 5, 5, 2, 2, 2, 1, 1, 1, 7, 25, 25, 25, 82, 99, 186, 187, 187, 187, 187, 1, 1, 5, 7, 7, 5, 5, 2, 7, 7, 25, 82, 82, 187, 1, 1, 1, 1, 5] 201
rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41])
total number of confs: 499
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051194 none NC(=O)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 4, 4, 5, 5, 17, 46, 46, 46, 112, 129, 195, 196, 196, 196, 196, 5, 5, 1, 3, 3, 1, 1, 5, 17, 17, 46, 112, 112, 196, 5, 5, 5, 5, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 25, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 589
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051194 none NC(=O)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 196, 201, 196, 196, 196, 187, 187, 187, 187, 125, 56, 56, 29, 56, 13, 1, 1, 1, 1, 1, 1, 1, 187, 187, 196, 201, 201, 196, 196, 187, 125, 125, 56, 29, 29, 1, 187, 187, 187, 187, 196] 201
rigid atoms, others: [36, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41])
total number of confs: 743
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051194 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051194
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051194/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051194
Building REAL300025051195
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051195'
/scratch/stefan/7786831/working/building/REAL300025051195 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051195

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051195/0 /scratch/stefan/7786831/working/building/REAL300025051195 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 51)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/51
`/scratch/stefan/7786831/working/3D/51' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H](C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)[NH+](C)C)

`REAL300025051195.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051195.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051195/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051195 none CC[C@@H](C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)[NH+](C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [20, 20, 19, 20, 19, 19, 19, 19, 18, 18, 13, 18, 9, 1, 1, 1, 1, 1, 1, 1, 19, 19, 20, 20, 20, 20, 20, 20, 20, 20, 20, 19, 19, 19, 18, 13, 13, 1, 19, 19, 19, 19, 20, 20, 20, 20, 20, 20] 20
rigid atoms, others: [37, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 62
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: REAL300025051195 none CC[C@@H](C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)[NH+](C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 2, 6, 2, 2, 1, 1, 1, 4, 8, 8, 8, 16, 16, 19, 19, 19, 19, 19, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 4, 4, 8, 16, 16, 19, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7] 20
rigid atoms, others: [6, 38, 7, 8, 41, 39, 40, 20, 21] set([0, 1, 2, 3, 4, 5, 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, 36, 37, 42, 43, 44, 45, 46, 47])
total number of confs: 107
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051195 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051195
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051195/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051195
Building REAL300025051196
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051196'
/scratch/stefan/7786831/working/building/REAL300025051196 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051196

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051196/0 /scratch/stefan/7786831/working/building/REAL300025051196 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 52)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/52
`/scratch/stefan/7786831/working/3D/52' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C(C)(F)F)

`REAL300025051196.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051196.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051196/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051196 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C(C)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 15, 15, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [191, 144, 144, 144, 144, 123, 64, 64, 34, 64, 13, 1, 1, 1, 1, 1, 1, 1, 144, 144, 191, 201, 201, 201, 191, 191, 191, 191, 144, 123, 123, 64, 34, 34, 1, 144, 144, 144, 144, 201, 201, 201] 201
rigid atoms, others: [34, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 869
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051196 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C(C)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 15, 15, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 2, 2, 2, 1, 1, 1, 4, 17, 17, 17, 42, 48, 144, 144, 144, 144, 144, 1, 1, 9, 20, 21, 21, 9, 9, 9, 9, 2, 4, 4, 17, 42, 42, 144, 1, 1, 1, 1, 21, 21, 21] 201
rigid atoms, others: [35, 4, 5, 6, 18, 19, 36, 38, 37] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41])
total number of confs: 383
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051196 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051196
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051196/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051196
Building REAL300025051197
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051197'
/scratch/stefan/7786831/working/building/REAL300025051197 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051197

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051197/0 /scratch/stefan/7786831/working/building/REAL300025051197 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 53)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/53
`/scratch/stefan/7786831/working/3D/53' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C)=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N1)

`REAL300025051197.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051197.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051197/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051197 none CC1=NC(C)=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 8, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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: [8, 8, 8, 8, 8, 2, 2, 2, 1, 1, 1, 7, 27, 27, 27, 73, 93, 173, 174, 174, 174, 174, 1, 1, 8, 8, 8, 8, 8, 8, 8, 2, 7, 7, 27, 73, 73, 174, 1, 1, 1, 1, 8] 201
rigid atoms, others: [38, 39, 8, 9, 10, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 42])
total number of confs: 455
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051197 none CC1=NC(C)=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 8, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 20, 50, 50, 50, 108, 133, 201, 201, 201, 201, 201, 8, 8, 1, 2, 2, 2, 2, 2, 2, 8, 20, 20, 50, 108, 108, 201, 8, 8, 8, 8, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 596
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051197 none CC1=NC(C)=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 8, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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, 174, 174, 174, 174, 129, 78, 78, 33, 78, 13, 1, 1, 1, 1, 1, 1, 1, 174, 174, 201, 201, 201, 201, 201, 201, 201, 174, 129, 129, 78, 33, 33, 1, 174, 174, 174, 174, 201] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 681
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051197 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051197
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051197/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051197
Building REAL300025051198
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051198'
/scratch/stefan/7786831/working/building/REAL300025051198 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051198

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051198/0 /scratch/stefan/7786831/working/building/REAL300025051198 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 54)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/54
`/scratch/stefan/7786831/working/3D/54' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=CN3C=CN=C23)CC1)

`REAL300025051198.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051198.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051198/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051198 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=CN3C=CN=C23)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 17, 56, 64, 149, 149, 149, 149, 149, 5, 1, 1, 1, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 56, 56, 149, 17, 5, 5, 3, 22, 22, 22, 22, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 365
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051198 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=CN3C=CN=C23)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [74, 33, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 125, 149, 149, 149, 149, 201, 201, 201, 201, 201, 201, 201, 201, 149, 149, 33, 33, 1, 74, 125, 125, 149, 201, 201, 201, 201, 149, 149, 149, 149] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 653
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051198 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=CN3C=CN=C23)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [79, 79, 79, 143, 152, 201, 201, 201, 201, 201, 31, 22, 13, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 143, 143, 201, 79, 31, 31, 13, 1, 1, 1, 1, 22, 22, 22, 22] 201
rigid atoms, others: [34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 662
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051198 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051198
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051198/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051198
Building REAL300025051199
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051199'
/scratch/stefan/7786831/working/building/REAL300025051199 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051199

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051199/0 /scratch/stefan/7786831/working/building/REAL300025051199 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 55)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/55
`/scratch/stefan/7786831/working/3D/55' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1)

`REAL300025051199.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051199.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051199/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051199 none CC1=NN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 8, 2, 2, 2, 1, 1, 1, 6, 16, 16, 16, 53, 69, 159, 159, 159, 159, 159, 1, 1, 12, 12, 12, 12, 12, 8, 8, 2, 6, 6, 16, 53, 53, 159, 1, 1, 1, 1, 12, 12] 201
rigid atoms, others: [37, 38, 7, 8, 9, 39, 40, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 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, 41, 42])
total number of confs: 394
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051199 none CC1=NN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 5, 12, 12, 12, 12, 29, 55, 55, 55, 109, 124, 201, 201, 201, 201, 201, 12, 12, 1, 1, 2, 2, 2, 5, 5, 12, 29, 29, 55, 109, 109, 201, 12, 12, 12, 12, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 41, 42, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 622
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051199 none CC1=NN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 159, 159, 159, 159, 110, 57, 57, 28, 57, 13, 1, 1, 1, 1, 1, 1, 1, 159, 159, 201, 201, 201, 201, 201, 201, 201, 159, 110, 110, 57, 28, 28, 1, 159, 159, 159, 159, 201, 201] 201
rigid atoms, others: [36, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42])
total number of confs: 811
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051199 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051199
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051199/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051199
Building REAL300025051200
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051200'
/scratch/stefan/7786831/working/building/REAL300025051200 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051200

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051200/0 /scratch/stefan/7786831/working/building/REAL300025051200 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 56)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/56
`/scratch/stefan/7786831/working/3D/56' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3C=CNC3=CC=N2)CC1)

`REAL300025051200.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051200.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051200/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051200 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3C=CNC3=CC=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 84, 91, 197, 197, 197, 197, 197, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 84, 84, 197, 27, 6, 6, 3, 7, 7, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 492
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051200 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3C=CNC3=CC=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [59, 33, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 151, 197, 197, 197, 197, 201, 201, 201, 201, 201, 201, 201, 201, 197, 197, 33, 33, 1, 59, 151, 151, 197, 201, 201, 201, 201, 201, 197, 197, 197, 197] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 747
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051200 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3C=CNC3=CC=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [53, 53, 53, 132, 137, 201, 201, 201, 201, 201, 13, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 132, 132, 201, 53, 13, 13, 4, 1, 1, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42])
total number of confs: 633
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051200 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051200
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051200/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051200
Building REAL300025051201
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051201'
/scratch/stefan/7786831/working/building/REAL300025051201 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051201

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051201/0 /scratch/stefan/7786831/working/building/REAL300025051201 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 57)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/57
`/scratch/stefan/7786831/working/3D/57' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(=O)NC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051201.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051201.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051201/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051201 none COC1=CC(=O)NC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 12, 1, 1, 1, 11, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 6, 23, 23, 23, 62, 69, 174, 174, 174, 174, 174, 1, 1, 7, 7, 7, 5, 5, 5, 2, 6, 6, 23, 62, 62, 174, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 408
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051201 none COC1=CC(=O)NC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 12, 1, 1, 1, 11, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 18, 50, 50, 50, 106, 113, 201, 201, 201, 201, 201, 5, 5, 3, 3, 3, 1, 1, 1, 5, 18, 18, 50, 106, 106, 201, 5, 5, 5, 5] 201
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: 575
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051201 none COC1=CC(=O)NC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 12, 1, 1, 1, 11, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 174, 174, 174, 174, 111, 43, 43, 27, 43, 13, 1, 1, 1, 1, 1, 1, 1, 174, 174, 201, 201, 201, 201, 201, 201, 174, 111, 111, 43, 27, 27, 1, 174, 174, 174, 174] 201
rigid atoms, others: [39, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 717
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051201 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051201
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051201/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051201
Building REAL300025051202
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051202'
/scratch/stefan/7786831/working/building/REAL300025051202 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051202

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051202/0 /scratch/stefan/7786831/working/building/REAL300025051202 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 58)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/58
`/scratch/stefan/7786831/working/3D/58' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=NC=C1[C@@H]1C[C@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051202.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051202.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051202/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051202 none CN1C=NC=C1[C@@H]1C[C@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 20, 33, 33, 33, 85, 115, 195, 195, 195, 195, 195, 9, 9, 7, 7, 7, 7, 7, 1, 1, 9, 20, 20, 33, 85, 85, 195, 9, 9, 9, 9] 201
rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 551
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051202 none CN1C=NC=C1[C@@H]1C[C@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 21, 21, 21, 21, 34, 52, 52, 52, 115, 137, 201, 201, 201, 201, 201, 21, 21, 2, 2, 2, 1, 1, 7, 7, 21, 34, 34, 52, 115, 115, 201, 21, 21, 21, 21] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 33] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 654
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051202 none CN1C=NC=C1[C@@H]1C[C@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 195, 195, 195, 195, 139, 195, 139, 139, 139, 106, 69, 69, 32, 69, 13, 1, 1, 1, 1, 1, 1, 1, 139, 139, 201, 201, 201, 201, 201, 195, 195, 139, 106, 106, 69, 32, 32, 1, 139, 139, 139, 139] 201
rigid atoms, others: [42, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46])
total number of confs: 753
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051202 none CN1C=NC=C1[C@@H]1C[C@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 21, 21, 21, 21, 9, 9, 9, 9, 2, 9, 2, 2, 1, 1, 1, 4, 9, 9, 9, 28, 40, 139, 139, 139, 139, 139, 1, 1, 21, 21, 21, 21, 21, 9, 9, 2, 4, 4, 9, 28, 28, 139, 1, 1, 1, 1] 201
rigid atoms, others: [45, 43, 44, 13, 14, 15, 46, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 288
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051202 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051202
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051202/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051202
Building REAL300025051203
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051203'
/scratch/stefan/7786831/working/building/REAL300025051203 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051203

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051203/0 /scratch/stefan/7786831/working/building/REAL300025051203 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 59)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/59
`/scratch/stefan/7786831/working/3D/59' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=NNN=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051203.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051203.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051203/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051203 none O=C(CCC1=NNN=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 8, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [2, 2, 2, 5, 6, 7, 7, 7, 7, 1, 1, 1, 5, 6, 6, 6, 16, 26, 47, 47, 47, 47, 47, 1, 1, 5, 5, 6, 6, 7, 7, 2, 5, 5, 6, 16, 16, 47, 1, 1, 1, 1] 49
rigid atoms, others: [38, 39, 40, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 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: REAL300025051203 none O=C(CCC1=NNN=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 8, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [7, 7, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 8, 9, 9, 9, 21, 31, 49, 49, 49, 49, 49, 7, 7, 7, 7, 5, 5, 1, 1, 7, 8, 8, 9, 21, 21, 49, 7, 7, 7, 7] 49
rigid atoms, others: [3, 4, 5, 6, 7, 8, 29, 30] set([0, 1, 2, 9, 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])
total number of confs: 138
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051203 none O=C(CCC1=NNN=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 8, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [47, 47, 47, 49, 49, 49, 49, 49, 49, 47, 45, 38, 38, 25, 38, 12, 1, 1, 1, 1, 1, 1, 1, 47, 47, 49, 49, 49, 49, 49, 49, 47, 45, 45, 38, 25, 25, 1, 47, 47, 47, 47] 49
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41])
total number of confs: 178
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051203 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051203/1 /scratch/stefan/7786831/working/building/REAL300025051203 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 60)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/60
`/scratch/stefan/7786831/working/3D/60' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CNN=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051203.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051203.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051203/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051203 none O=C(CCC1=CNN=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 8, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [2, 2, 2, 4, 4, 6, 6, 6, 6, 1, 1, 1, 5, 8, 8, 8, 14, 20, 35, 35, 35, 35, 35, 1, 1, 4, 4, 4, 4, 6, 6, 2, 5, 5, 8, 14, 14, 35, 1, 1, 1, 1] 35
rigid atoms, others: [38, 39, 40, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 112
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051203 none O=C(CCC1=CNN=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 8, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [6, 4, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 8, 11, 11, 11, 15, 21, 35, 35, 35, 35, 35, 6, 6, 4, 4, 4, 4, 1, 1, 6, 8, 8, 11, 15, 15, 35, 6, 6, 6, 6] 35
rigid atoms, others: [3, 4, 5, 6, 7, 8, 29, 30] set([0, 1, 2, 9, 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])
total number of confs: 100
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051203 none O=C(CCC1=CNN=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 8, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 35, 31, 31, 21, 31, 12, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 31, 21, 21, 1, 35, 35, 35, 35] 35
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41])
total number of confs: 118
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051203 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051203
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051203/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051203/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051203
Building REAL300025051204
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051204'
/scratch/stefan/7786831/working/building/REAL300025051204 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051204

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051204/0 /scratch/stefan/7786831/working/building/REAL300025051204 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 61)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/61
`/scratch/stefan/7786831/working/3D/61' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C[C@@H]1OCC[C@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051204.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051204.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051204/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051204 none C=C[C@@H]1OCC[C@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [1, 1, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 8, 8, 8, 8, 8, 8, 2, 8, 2, 2, 1, 1, 1, 4, 11, 11, 11, 38, 66, 162, 162, 162, 162, 162, 1, 1, 17, 17, 17, 8, 8, 8, 8, 2, 4, 4, 11, 38, 38, 162, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 42, 11, 12, 13, 44, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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])
total number of confs: 374
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051204 none C=C[C@@H]1OCC[C@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [1, 1, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 16, 31, 31, 31, 76, 110, 201, 201, 201, 201, 201, 8, 8, 6, 6, 6, 1, 1, 1, 1, 8, 16, 16, 31, 76, 76, 201, 8, 8, 8, 8] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 33, 30, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 528
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051204 none C=C[C@@H]1OCC[C@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [1, 1, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 162, 201, 162, 162, 162, 132, 77, 77, 29, 77, 12, 1, 1, 1, 1, 1, 1, 1, 162, 162, 201, 201, 201, 201, 201, 201, 201, 162, 132, 132, 77, 29, 29, 1, 162, 162, 162, 162] 201
rigid atoms, others: [40, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 776
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051204 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051204
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051204/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051204
Building REAL300025051205
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051205'
/scratch/stefan/7786831/working/building/REAL300025051205 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051205

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051205/0 /scratch/stefan/7786831/working/building/REAL300025051205 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 62)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/62
`/scratch/stefan/7786831/working/3D/62' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C[C@@H]1C[C@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051205.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051205.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051205/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051205 none CC(C)C[C@@H]1C[C@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 26, 26, 11, 11, 11, 11, 2, 11, 2, 2, 1, 1, 1, 4, 7, 7, 7, 20, 28, 93, 93, 93, 93, 93, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 11, 11, 2, 4, 4, 7, 20, 20, 93, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 46, 45, 48, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
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: REAL300025051205 none CC(C)C[C@@H]1C[C@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 22, 29, 29, 29, 58, 81, 168, 168, 168, 168, 168, 11, 11, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 11, 22, 22, 29, 58, 58, 168, 11, 11, 11, 11] 201
rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 4, 37] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 446
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051205 none CC(C)C[C@@H]1C[C@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 168, 168, 168, 168, 93, 168, 93, 93, 93, 86, 50, 50, 24, 50, 12, 1, 1, 1, 1, 1, 1, 1, 93, 93, 201, 201, 201, 201, 201, 201, 201, 201, 201, 168, 168, 93, 86, 86, 50, 24, 24, 1, 93, 93, 93, 93] 201
rigid atoms, others: [44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48])
total number of confs: 811
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051205 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051205
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051205/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051205
Building REAL300025051206
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051206'
/scratch/stefan/7786831/working/building/REAL300025051206 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051206

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051206/0 /scratch/stefan/7786831/working/building/REAL300025051206 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 63)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/63
`/scratch/stefan/7786831/working/3D/63' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1C[C@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051206.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051206.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051206/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051206 none CC[C@@H]1C[C@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 11, 11, 11, 11, 2, 11, 2, 2, 1, 1, 1, 4, 8, 8, 8, 24, 33, 113, 113, 113, 113, 113, 1, 1, 20, 20, 20, 20, 20, 11, 11, 2, 4, 4, 8, 24, 24, 113, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 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: REAL300025051206 none CC[C@@H]1C[C@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 24, 36, 36, 36, 77, 99, 201, 201, 201, 201, 201, 11, 11, 3, 3, 3, 3, 3, 1, 1, 11, 24, 24, 36, 77, 77, 201, 11, 11, 11, 11] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 550
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051206 none CC[C@@H]1C[C@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 113, 201, 113, 113, 113, 95, 51, 51, 25, 51, 12, 1, 1, 1, 1, 1, 1, 1, 113, 113, 201, 201, 201, 201, 201, 201, 201, 113, 95, 95, 51, 25, 25, 1, 113, 113, 113, 113] 201
rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 744
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051206 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051206
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051206/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051206
Building REAL300025051207
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051207'
/scratch/stefan/7786831/working/building/REAL300025051207 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051207

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051207/0 /scratch/stefan/7786831/working/building/REAL300025051207 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 64)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/64
`/scratch/stefan/7786831/working/3D/64' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]3CC[C@@H]2O3)CC1)

`REAL300025051207.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051207.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051207/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051207 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]3CC[C@@H]2O3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 31, 31, 104, 123, 197, 197, 197, 197, 197, 7, 1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 104, 104, 197, 31, 7, 7, 3, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 42, 11, 12, 13, 44, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 559
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051207 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]3CC[C@@H]2O3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 35, 12, 1, 1, 1, 1, 1, 1, 1, 84, 84, 165, 197, 197, 197, 197, 201, 201, 201, 201, 201, 201, 201, 201, 201, 197, 197, 35, 35, 1, 84, 165, 165, 197, 201, 201, 201, 201, 201, 201, 197, 197, 197, 197] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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])
total number of confs: 750
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051207 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]3CC[C@@H]2O3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 139, 152, 201, 201, 201, 201, 201, 20, 12, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 139, 139, 201, 57, 20, 20, 9, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12] 201
rigid atoms, others: [35, 36, 37, 38, 39, 40, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44])
total number of confs: 630
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051207 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051207
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051207/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051207
Building REAL300025051208
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051208'
/scratch/stefan/7786831/working/building/REAL300025051208 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051208

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051208/0 /scratch/stefan/7786831/working/building/REAL300025051208 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 65)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/65
`/scratch/stefan/7786831/working/3D/65' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCC(=O)N1)

`REAL300025051208.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051208.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051208/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051208 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 179, 179, 179, 179, 132, 56, 56, 29, 56, 13, 1, 1, 1, 1, 1, 1, 1, 179, 179, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 179, 132, 132, 56, 29, 29, 1, 179, 179, 179, 179, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [36, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 813
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051208 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 2, 2, 2, 1, 1, 1, 7, 24, 24, 24, 65, 77, 179, 179, 179, 179, 179, 1, 1, 5, 6, 6, 6, 6, 6, 5, 5, 5, 5, 2, 7, 7, 24, 65, 65, 179, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6] 201
rigid atoms, others: [4, 5, 6, 39, 40, 18, 19, 38, 37] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46])
total number of confs: 447
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051208 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 6, 6, 6, 6, 19, 49, 49, 49, 107, 126, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 19, 19, 49, 107, 107, 201, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 609
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051208 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051208
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051208/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051208
Building REAL300025051209
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051209'
/scratch/stefan/7786831/working/building/REAL300025051209 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051209

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051209/0 /scratch/stefan/7786831/working/building/REAL300025051209 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 66)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/66
`/scratch/stefan/7786831/working/3D/66' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C([C@@H]2C[C@H]2C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1)

`REAL300025051209.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051209.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051209/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051209 none CN1C=C([C@@H]2C[C@H]2C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 19, 31, 31, 31, 80, 108, 174, 174, 174, 174, 174, 11, 11, 8, 8, 8, 8, 8, 8, 1, 1, 11, 19, 19, 31, 80, 80, 174, 11, 11, 11, 11, 8] 201
rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 509
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051209 none CN1C=C([C@@H]2C[C@H]2C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 29, 29, 29, 29, 40, 60, 60, 60, 113, 141, 201, 201, 201, 201, 201, 29, 29, 1, 1, 2, 2, 2, 1, 8, 8, 29, 40, 40, 60, 113, 113, 201, 29, 29, 29, 29, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 32, 46, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 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, 40, 41, 42, 43, 44, 45])
total number of confs: 643
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051209 none CN1C=C([C@@H]2C[C@H]2C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 174, 174, 174, 174, 104, 174, 104, 104, 104, 93, 64, 64, 31, 64, 13, 1, 1, 1, 1, 1, 1, 1, 104, 104, 201, 201, 201, 201, 201, 201, 174, 174, 104, 93, 93, 64, 31, 31, 1, 104, 104, 104, 104, 201] 201
rigid atoms, others: [41, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46])
total number of confs: 681
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051209 none CN1C=C([C@@H]2C[C@H]2C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 29, 11, 11, 11, 11, 2, 11, 2, 2, 1, 1, 1, 3, 6, 6, 6, 19, 31, 104, 104, 104, 104, 104, 1, 1, 29, 29, 29, 29, 29, 29, 11, 11, 2, 3, 3, 6, 19, 19, 104, 1, 1, 1, 1, 29] 201
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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, 46])
total number of confs: 242
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051209 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051209
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051209/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051209
Building REAL300025051210
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051210'
/scratch/stefan/7786831/working/building/REAL300025051210 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051210

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051210/0 /scratch/stefan/7786831/working/building/REAL300025051210 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 67)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/67
`/scratch/stefan/7786831/working/3D/67' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2=CC=CO2)CC1)

`REAL300025051210.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051210.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051210/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051210 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2=CC=CO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 15, 33, 38, 84, 84, 84, 84, 84, 5, 1, 1, 1, 3, 3, 3, 21, 21, 21, 21, 21, 80, 80, 80, 80, 1, 1, 33, 33, 84, 15, 5, 5, 3, 21, 21, 80, 80, 80, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 323
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051210 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2=CC=CO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 27, 12, 1, 1, 1, 1, 1, 1, 1, 38, 38, 71, 84, 84, 84, 84, 174, 174, 174, 174, 174, 201, 201, 201, 201, 84, 84, 27, 27, 1, 38, 71, 71, 84, 174, 174, 201, 201, 201, 84, 84, 84, 84] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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])
total number of confs: 634
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051210 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2=CC=CO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [157, 157, 157, 191, 192, 201, 201, 201, 201, 201, 93, 80, 63, 63, 10, 63, 10, 10, 10, 1, 10, 1, 1, 1, 1, 1, 80, 80, 191, 191, 201, 157, 93, 93, 63, 10, 10, 1, 1, 1, 80, 80, 80, 80] 201
rigid atoms, others: [37, 38, 39, 19, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43])
total number of confs: 726
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051210 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2=CC=CO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 139, 143, 174, 174, 174, 174, 174, 31, 21, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 21, 21, 139, 139, 174, 82, 31, 31, 12, 1, 1, 10, 10, 10, 21, 21, 21, 21] 201
rigid atoms, others: [35, 36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 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
/scratch/stefan/7786831/working/building/REAL300025051210 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051210
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051210/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051210
Building REAL300025051211
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051211'
/scratch/stefan/7786831/working/building/REAL300025051211 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051211

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051211/0 /scratch/stefan/7786831/working/building/REAL300025051211 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 68)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/68
`/scratch/stefan/7786831/working/3D/68' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2=CC=CN=C2)CC1)

`REAL300025051211.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051211.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051211/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051211 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2=CC=CN=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 14, 35, 41, 80, 80, 80, 80, 80, 5, 1, 1, 1, 3, 3, 3, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 1, 1, 35, 35, 80, 14, 5, 5, 3, 22, 22, 50, 50, 50, 50, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 299
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051211 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2=CC=CN=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [41, 26, 12, 1, 1, 1, 1, 1, 1, 1, 41, 41, 70, 80, 80, 80, 80, 158, 158, 158, 158, 158, 201, 201, 201, 201, 201, 80, 80, 26, 26, 1, 41, 70, 70, 80, 158, 158, 201, 201, 201, 201, 80, 80, 80, 80] 201
rigid atoms, others: [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, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 628
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051211 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2=CC=CN=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [121, 121, 121, 182, 186, 201, 201, 201, 201, 201, 64, 50, 32, 32, 6, 32, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 50, 50, 182, 182, 201, 121, 64, 64, 32, 6, 6, 1, 1, 1, 1, 50, 50, 50, 50] 201
rigid atoms, others: [38, 39, 40, 41, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45])
total number of confs: 783
number of broken/clashed sets: 1
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051211 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2=CC=CN=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 130, 134, 158, 158, 158, 158, 158, 32, 22, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 22, 22, 130, 130, 158, 77, 32, 32, 12, 1, 1, 6, 6, 6, 6, 22, 22, 22, 22] 201
rigid atoms, others: [36, 37, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 598
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051211 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051211
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051211/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051211
Building REAL300025051212
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051212'
/scratch/stefan/7786831/working/building/REAL300025051212 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051212

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051212/0 /scratch/stefan/7786831/working/building/REAL300025051212 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 69)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/69
`/scratch/stefan/7786831/working/3D/69' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3NC=CC3=CC=C2)CC1)

`REAL300025051212.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051212.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051212/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051212 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3NC=CC3=CC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 25, 84, 96, 169, 169, 169, 169, 169, 6, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 84, 84, 169, 25, 6, 6, 3, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 466
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051212 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3NC=CC3=CC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [71, 32, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 125, 169, 169, 169, 169, 201, 201, 201, 201, 201, 201, 201, 201, 169, 169, 32, 32, 1, 71, 125, 125, 169, 201, 201, 201, 201, 201, 201, 169, 169, 169, 169] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 674
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051212 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3NC=CC3=CC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 150, 161, 201, 201, 201, 201, 201, 21, 13, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 150, 150, 201, 65, 21, 21, 8, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43])
total number of confs: 673
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051212 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051212
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051212/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051212
Building REAL300025051213
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051213'
/scratch/stefan/7786831/working/building/REAL300025051213 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051213

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051213/0 /scratch/stefan/7786831/working/building/REAL300025051213 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 70)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/70
`/scratch/stefan/7786831/working/3D/70' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051213.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051213.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051213/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051213 none CC(C)C1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 4, 6, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 23, 23, 23, 71, 83, 198, 198, 198, 198, 198, 1, 1, 4, 6, 6, 6, 6, 6, 6, 6, 4, 2, 7, 7, 23, 71, 71, 198, 1, 1, 1, 1, 4] 201
rigid atoms, others: [43, 9, 10, 11, 44, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45])
total number of confs: 483
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051213 none CC(C)C1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 4, 4, 4, 4, 12, 29, 29, 29, 80, 93, 201, 201, 201, 201, 201, 4, 4, 1, 3, 3, 3, 3, 3, 3, 3, 1, 4, 12, 12, 29, 80, 80, 201, 4, 4, 4, 4, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 33, 7, 45, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 514
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051213 none CC(C)C1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 198, 198, 198, 141, 56, 56, 30, 56, 13, 1, 1, 1, 1, 1, 1, 1, 198, 198, 201, 201, 201, 201, 201, 201, 201, 201, 201, 198, 141, 141, 56, 30, 30, 1, 198, 198, 198, 198, 201] 201
rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45])
total number of confs: 757
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051213 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051213
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051213/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051213
Building REAL300025051214
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051214'
/scratch/stefan/7786831/working/building/REAL300025051214 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051214

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051214/0 /scratch/stefan/7786831/working/building/REAL300025051214 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 71)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/71
`/scratch/stefan/7786831/working/3D/71' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(Cl)=C1)

`REAL300025051214.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051214.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051214/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051214 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 2, 7, 7, 2, 2, 2, 1, 1, 1, 4, 21, 21, 21, 86, 106, 157, 157, 157, 157, 157, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 2, 4, 4, 21, 86, 86, 157, 1, 1, 1, 1, 7] 201
rigid atoms, others: [38, 7, 8, 9, 39, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 42])
total number of confs: 464
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051214 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 7, 7, 17, 59, 59, 59, 143, 164, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 2, 2, 2, 1, 1, 7, 17, 17, 59, 143, 143, 201, 7, 7, 7, 7, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 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])
total number of confs: 653
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051214 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 157, 201, 201, 157, 157, 157, 157, 128, 69, 69, 22, 69, 12, 1, 1, 1, 1, 1, 1, 1, 157, 157, 201, 201, 201, 201, 201, 201, 201, 201, 157, 128, 128, 69, 22, 22, 1, 157, 157, 157, 157, 201] 201
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 868
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051214 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051214
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051214/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051214
Building REAL300025051215
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051215'
/scratch/stefan/7786831/working/building/REAL300025051215 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051215

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051215/0 /scratch/stefan/7786831/working/building/REAL300025051215 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 72)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/72
`/scratch/stefan/7786831/working/3D/72' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(NC(C)=O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051215.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051215.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051215/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051215 none CCC(NC(C)=O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 5, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [199, 192, 137, 192, 201, 201, 201, 137, 137, 137, 108, 62, 62, 33, 62, 13, 1, 1, 1, 1, 1, 1, 1, 137, 137, 201, 201, 201, 201, 201, 192, 201, 201, 201, 201, 137, 108, 108, 62, 33, 33, 1, 137, 137, 137, 137] 201
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 909
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051215 none CCC(NC(C)=O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 5, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 7, 2, 7, 11, 11, 11, 2, 2, 1, 1, 1, 7, 14, 14, 14, 40, 59, 137, 137, 137, 137, 137, 1, 1, 11, 11, 11, 11, 11, 7, 11, 11, 11, 11, 2, 7, 7, 14, 40, 40, 137, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 369
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051215 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051215
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051215/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051215
Building REAL300025051216
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051216'
/scratch/stefan/7786831/working/building/REAL300025051216 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051216

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051216/0 /scratch/stefan/7786831/working/building/REAL300025051216 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 73)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/73
`/scratch/stefan/7786831/working/3D/73' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=C1F)

`REAL300025051216.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051216.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051216/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051216 none COC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 13, 13, 13, 38, 47, 116, 116, 116, 116, 116, 1, 1, 5, 5, 5, 5, 11, 11, 11, 5, 2, 4, 4, 13, 38, 38, 116, 1, 1, 1, 1, 5, 5] 201
rigid atoms, others: [38, 7, 8, 9, 39, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 42, 43])
total number of confs: 272
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051216 none COC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 37, 37, 37, 82, 95, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 1, 4, 4, 4, 1, 5, 13, 13, 37, 82, 82, 201, 5, 5, 5, 5, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 42, 43, 23, 24, 25, 26, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 519
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051216 none COC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 116, 116, 116, 95, 65, 65, 31, 65, 13, 1, 1, 1, 1, 1, 1, 1, 116, 116, 201, 201, 201, 201, 201, 201, 201, 201, 116, 95, 95, 65, 31, 31, 1, 116, 116, 116, 116, 201, 201] 201
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43])
total number of confs: 577
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051216 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051216
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051216/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051216
Building REAL300025051217
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051217'
/scratch/stefan/7786831/working/building/REAL300025051217 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051217

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051217/0 /scratch/stefan/7786831/working/building/REAL300025051217 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 74)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/74
`/scratch/stefan/7786831/working/3D/74' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3C=CNC3=CC=C2)CC1)

`REAL300025051217.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051217.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051217/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051217 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3C=CNC3=CC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 15, 51, 59, 134, 134, 134, 134, 134, 5, 1, 1, 1, 3, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 51, 51, 134, 15, 5, 5, 3, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 336
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051217 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3C=CNC3=CC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [63, 31, 13, 1, 1, 1, 1, 1, 1, 1, 63, 63, 118, 134, 134, 134, 134, 201, 201, 201, 201, 201, 201, 201, 201, 134, 134, 31, 31, 1, 63, 118, 118, 134, 201, 201, 201, 201, 201, 201, 134, 134, 134, 134] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 623
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051217 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3C=CNC3=CC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [66, 66, 66, 139, 147, 201, 201, 201, 201, 201, 28, 18, 10, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 139, 139, 201, 66, 28, 28, 10, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43])
total number of confs: 670
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051217 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051217
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051217/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051217
Building REAL300025051218
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051218'
/scratch/stefan/7786831/working/building/REAL300025051218 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051218

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051218/0 /scratch/stefan/7786831/working/building/REAL300025051218 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 75)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/75
`/scratch/stefan/7786831/working/3D/75' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)=CCCC(C)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051218.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051218.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051218/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051218 none CC(C)=CCCC(C)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 194, 171, 145, 96, 144, 35, 35, 35, 35, 27, 25, 25, 19, 25, 13, 1, 1, 1, 1, 1, 1, 1, 35, 35, 201, 201, 201, 201, 201, 201, 201, 194, 194, 171, 171, 146, 146, 146, 146, 96, 96, 35, 27, 27, 25, 19, 19, 1, 35, 35, 35, 35] 201
rigid atoms, others: [50, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54])
total number of confs: 944
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: REAL300025051218 none CC(C)=CCCC(C)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 61, 61, 54, 43, 24, 11, 24, 2, 2, 2, 1, 1, 1, 4, 7, 7, 7, 10, 13, 35, 35, 35, 35, 35, 1, 1, 61, 61, 61, 61, 61, 61, 61, 54, 54, 43, 43, 25, 25, 25, 25, 11, 11, 2, 4, 4, 7, 10, 10, 35, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 51, 52, 53, 54, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 371
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051218 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051218
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051218/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051218
Building REAL300025051219
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051219'
/scratch/stefan/7786831/working/building/REAL300025051219 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051219

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051219/0 /scratch/stefan/7786831/working/building/REAL300025051219 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 76)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/76
`/scratch/stefan/7786831/working/3D/76' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(F)=C1F)

`REAL300025051219.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051219.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051219/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051219 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(F)=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 15, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 7, 29, 29, 29, 81, 94, 193, 193, 193, 193, 193, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 7, 7, 29, 81, 81, 193, 1, 1, 1, 1] 201
rigid atoms, others: [39, 8, 9, 42, 7, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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])
total number of confs: 503
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051219 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(F)=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 15, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 19, 59, 59, 59, 127, 138, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 1, 2, 2, 2, 1, 1, 5, 19, 19, 59, 127, 127, 201, 5, 5, 5, 5] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 23, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 638
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051219 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(F)=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 15, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 193, 193, 193, 193, 122, 48, 48, 24, 48, 11, 1, 1, 1, 1, 1, 1, 1, 193, 193, 201, 201, 201, 201, 201, 201, 201, 201, 201, 193, 122, 122, 48, 24, 24, 1, 193, 193, 193, 193] 201
rigid atoms, others: [38, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 710
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051219 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051219
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051219/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051219
Building REAL300025051220
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051220'
/scratch/stefan/7786831/working/building/REAL300025051220 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051220

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051220/0 /scratch/stefan/7786831/working/building/REAL300025051220 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 77)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/77
`/scratch/stefan/7786831/working/3D/77' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1)

`REAL300025051220.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051220.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051220/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051220 none C=CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [10, 2, 3, 5, 5, 2, 2, 2, 1, 1, 1, 5, 9, 9, 9, 17, 37, 117, 117, 117, 117, 117, 1, 1, 5, 5, 10, 10, 10, 5, 5, 2, 5, 5, 9, 17, 17, 117, 1, 1, 1, 1, 5, 5] 144
rigid atoms, others: [38, 39, 8, 9, 10, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 42, 43])
total number of confs: 236
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051220 none C=CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 23, 23, 23, 44, 80, 144, 144, 144, 144, 144, 5, 5, 1, 1, 4, 4, 4, 1, 1, 5, 12, 12, 23, 44, 44, 144, 5, 5, 5, 5, 1, 1] 144
rigid atoms, others: [1, 2, 3, 4, 5, 6, 42, 43, 24, 25, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 361
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051220 none C=CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [144, 117, 138, 144, 144, 117, 117, 117, 117, 94, 79, 79, 38, 79, 13, 1, 1, 1, 1, 1, 1, 1, 117, 117, 144, 144, 144, 144, 144, 144, 144, 117, 94, 94, 79, 38, 38, 1, 117, 117, 117, 117, 144, 144] 144
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43])
total number of confs: 637
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051220 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051220
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051220/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051220
Building REAL300025051221
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051221'
/scratch/stefan/7786831/working/building/REAL300025051221 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051221

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051221/0 /scratch/stefan/7786831/working/building/REAL300025051221 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 78)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/78
`/scratch/stefan/7786831/working/3D/78' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051221.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051221.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051221/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051221 none CC(C)CCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 185, 185, 194, 91, 91, 91, 91, 82, 47, 47, 23, 47, 12, 1, 1, 1, 1, 1, 1, 1, 91, 91, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 194, 194, 91, 82, 82, 47, 23, 23, 1, 91, 91, 91, 91] 201
rigid atoms, others: [43, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47])
total number of confs: 1075
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051221 none CC(C)CCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 15, 15, 10, 2, 2, 2, 1, 1, 1, 4, 8, 8, 8, 24, 33, 91, 91, 91, 91, 91, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 2, 4, 4, 8, 24, 24, 91, 1, 1, 1, 1] 201
rigid atoms, others: [8, 9, 10, 44, 45, 46, 47, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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: 304
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051221 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051221
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051221/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051221
Building REAL300025051222
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051222'
/scratch/stefan/7786831/working/building/REAL300025051222 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051222

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051222/0 /scratch/stefan/7786831/working/building/REAL300025051222 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 79)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/79
`/scratch/stefan/7786831/working/3D/79' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=C2OCC3)CC1)

`REAL300025051222.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051222.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051222/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051222 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=C2OCC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 87, 98, 194, 194, 194, 194, 194, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 87, 87, 194, 27, 6, 6, 3, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 42, 11, 12, 13, 44, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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])
total number of confs: 488
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051222 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=C2OCC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 33, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 148, 194, 194, 194, 194, 201, 201, 201, 201, 201, 201, 201, 201, 194, 194, 33, 33, 1, 71, 148, 148, 194, 201, 201, 201, 201, 201, 201, 201, 194, 194, 194, 194] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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: 742
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051222 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=C2OCC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [55, 55, 55, 136, 148, 201, 201, 201, 201, 201, 14, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 136, 136, 201, 55, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44])
total number of confs: 641
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051222 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051222
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051222/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051222
Building REAL300025051223
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051223'
/scratch/stefan/7786831/working/building/REAL300025051223 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051223

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051223/0 /scratch/stefan/7786831/working/building/REAL300025051223 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 80)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/80
`/scratch/stefan/7786831/working/3D/80' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3OCCC3=C2)CC1)

`REAL300025051223.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051223.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051223/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051223 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3OCCC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 57, 66, 107, 107, 107, 107, 107, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 57, 57, 107, 18, 5, 5, 3, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 42, 11, 12, 13, 44, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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])
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: REAL300025051223 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3OCCC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 27, 13, 1, 1, 1, 1, 1, 1, 1, 58, 58, 93, 107, 107, 107, 107, 201, 201, 201, 201, 201, 201, 201, 201, 107, 107, 27, 27, 1, 58, 93, 93, 107, 201, 201, 201, 201, 201, 201, 201, 107, 107, 107, 107] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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: 558
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051223 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3OCCC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 150, 166, 201, 201, 201, 201, 201, 17, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 150, 150, 201, 63, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44])
total number of confs: 692
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051223 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051223
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051223/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051223
Building REAL300025051224
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051224'
/scratch/stefan/7786831/working/building/REAL300025051224 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051224

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051224/0 /scratch/stefan/7786831/working/building/REAL300025051224 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 81)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/81
`/scratch/stefan/7786831/working/3D/81' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1C)

`REAL300025051224.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051224.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051224/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051224 none CC1=CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 9, 10, 10, 5, 2, 2, 2, 1, 1, 1, 6, 18, 18, 18, 49, 63, 121, 121, 121, 121, 121, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 2, 6, 6, 18, 49, 49, 121, 1, 1, 1, 1, 10, 10, 10, 10] 201
rigid atoms, others: [43, 8, 9, 10, 23, 44, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 45, 46, 47, 48])
total number of confs: 328
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051224 none CC1=CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 10, 10, 10, 10, 25, 45, 45, 45, 111, 128, 201, 201, 201, 201, 201, 10, 10, 1, 1, 1, 2, 2, 2, 1, 1, 3, 3, 10, 25, 25, 45, 111, 111, 201, 10, 10, 10, 10, 1, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 45, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48])
total number of confs: 608
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051224 none CC1=CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 200, 201, 201, 130, 121, 121, 121, 121, 95, 52, 52, 26, 52, 12, 1, 1, 1, 1, 1, 1, 1, 121, 121, 201, 201, 201, 201, 201, 201, 201, 201, 130, 130, 121, 95, 95, 52, 26, 26, 1, 121, 121, 121, 121, 201, 201, 201, 201] 201
rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 663
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051224 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051224
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051224/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051224
Building REAL300025051225
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051225'
/scratch/stefan/7786831/working/building/REAL300025051225 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051225

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051225/0 /scratch/stefan/7786831/working/building/REAL300025051225 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 82)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/82
`/scratch/stefan/7786831/working/3D/82' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C=NC=N2)CC1)

`REAL300025051225.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051225.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051225/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051225 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C=NC=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 12, 32, 40, 88, 88, 88, 88, 88, 5, 1, 1, 1, 3, 3, 3, 17, 55, 55, 55, 55, 1, 1, 32, 32, 88, 12, 5, 5, 3, 17, 17, 55, 55, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
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: REAL300025051225 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C=NC=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [51, 25, 13, 1, 1, 1, 1, 1, 1, 1, 51, 51, 81, 88, 88, 88, 88, 165, 201, 201, 201, 201, 88, 88, 25, 25, 1, 51, 81, 81, 88, 165, 165, 201, 201, 88, 88, 88, 88] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 767
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051225 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C=NC=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [131, 131, 131, 170, 183, 201, 201, 201, 201, 201, 71, 55, 46, 46, 9, 46, 1, 1, 1, 1, 1, 1, 55, 55, 170, 170, 201, 131, 71, 71, 46, 9, 9, 1, 1, 55, 55, 55, 55] 201
rigid atoms, others: [33, 34, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38])
total number of confs: 704
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051225 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051225
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051225/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051225
Building REAL300025051226
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051226'
/scratch/stefan/7786831/working/building/REAL300025051226 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051226

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051226/0 /scratch/stefan/7786831/working/building/REAL300025051226 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 83)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/83
`/scratch/stefan/7786831/working/3D/83' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CS1)

`REAL300025051226.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051226.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051226/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051226 none CC1=NC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 9, 2, 2, 2, 1, 1, 1, 6, 16, 16, 16, 60, 84, 159, 159, 159, 159, 159, 1, 1, 10, 10, 10, 10, 10, 9, 9, 2, 6, 6, 16, 60, 60, 159, 1, 1, 1, 1, 10] 201
rigid atoms, others: [37, 38, 7, 8, 9, 39, 40, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 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, 41])
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: REAL300025051226 none CC1=NC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 4, 10, 10, 10, 10, 23, 38, 38, 38, 96, 124, 201, 201, 201, 201, 201, 10, 10, 1, 1, 2, 2, 2, 4, 4, 10, 23, 23, 38, 96, 96, 201, 10, 10, 10, 10, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 41, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 580
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051226 none CC1=NC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 200, 159, 159, 159, 159, 120, 65, 65, 28, 65, 13, 1, 1, 1, 1, 1, 1, 1, 159, 159, 201, 201, 201, 201, 201, 200, 200, 159, 120, 120, 65, 28, 28, 1, 159, 159, 159, 159, 201] 201
rigid atoms, others: [36, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41])
total number of confs: 821
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051226 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051226
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051226/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051226
Building REAL300025051227
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051227'
/scratch/stefan/7786831/working/building/REAL300025051227 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051227

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051227/0 /scratch/stefan/7786831/working/building/REAL300025051227 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 84)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/84
`/scratch/stefan/7786831/working/3D/84' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCC1=CC=CS1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051227.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051227.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051227/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051227 none O=C(CCCC1=CC=CS1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 14, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 10, 15, 21, 29, 29, 29, 29, 1, 1, 1, 5, 7, 7, 7, 21, 28, 78, 78, 78, 78, 78, 1, 1, 10, 10, 19, 19, 21, 21, 29, 29, 29, 2, 5, 5, 7, 21, 21, 78, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
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: REAL300025051227 none O=C(CCCC1=CC=CS1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 14, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 9, 5, 3, 1, 1, 1, 1, 1, 1, 29, 29, 29, 49, 61, 61, 61, 97, 124, 201, 201, 201, 201, 201, 29, 29, 9, 9, 5, 5, 3, 3, 1, 1, 1, 29, 49, 49, 61, 97, 97, 201, 29, 29, 29, 29] 201
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 632
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051227 none O=C(CCCC1=CC=CS1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 14, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 159, 156, 174, 201, 201, 201, 201, 78, 70, 42, 42, 24, 42, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 159, 159, 173, 173, 174, 174, 201, 201, 201, 78, 70, 70, 42, 24, 24, 1, 78, 78, 78, 78] 201
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 885
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051227 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051227
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051227/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051227
Building REAL300025051228
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051228'
/scratch/stefan/7786831/working/building/REAL300025051228 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051228

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051228/0 /scratch/stefan/7786831/working/building/REAL300025051228 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 85)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/85
`/scratch/stefan/7786831/working/3D/85' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=C(C)C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1)

`REAL300025051228.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051228.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051228/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051228 none CCC1=C(C)C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 20, 20, 20, 56, 60, 114, 114, 114, 114, 114, 1, 1, 4, 7, 7, 7, 7, 7, 4, 4, 4, 4, 2, 7, 7, 20, 56, 56, 114, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
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: REAL300025051228 none CCC1=C(C)C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 3, 3, 4, 4, 10, 24, 24, 24, 60, 64, 114, 114, 114, 114, 114, 4, 4, 1, 3, 3, 3, 3, 3, 2, 2, 2, 1, 4, 10, 10, 24, 60, 60, 114, 4, 4, 4, 4] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 34, 25] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 350
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051228 none CCC1=C(C)C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 114, 114, 114, 114, 114, 114, 114, 114, 114, 73, 37, 37, 25, 37, 12, 1, 1, 1, 1, 1, 1, 1, 114, 114, 114, 201, 201, 201, 201, 201, 114, 114, 114, 114, 114, 73, 73, 37, 25, 25, 1, 114, 114, 114, 114] 201
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 950
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051228 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051228
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051228/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051228
Building REAL300025051229
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051229'
/scratch/stefan/7786831/working/building/REAL300025051229 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051229

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051229/0 /scratch/stefan/7786831/working/building/REAL300025051229 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 86)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/86
`/scratch/stefan/7786831/working/3D/86' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=NC=CN=C3C=C2)CC1)

`REAL300025051229.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051229.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051229/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051229 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=NC=CN=C3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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, 19, 19, 57, 67, 123, 123, 123, 123, 123, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 57, 57, 123, 19, 5, 5, 3, 9, 9, 9, 9, 9, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
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: REAL300025051229 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=NC=CN=C3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [52, 27, 13, 1, 1, 1, 1, 1, 1, 1, 52, 52, 100, 123, 123, 123, 123, 201, 201, 201, 201, 201, 201, 201, 201, 201, 123, 123, 27, 27, 1, 52, 100, 100, 123, 201, 201, 201, 201, 201, 123, 123, 123, 123] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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])
total number of confs: 587
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051229 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=NC=CN=C3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [61, 61, 61, 145, 156, 201, 201, 201, 201, 201, 17, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 145, 145, 201, 61, 17, 17, 5, 1, 1, 1, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43])
total number of confs: 678
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051229 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051229
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051229/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051229
Building REAL300025051230
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051230'
/scratch/stefan/7786831/working/building/REAL300025051230 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051230

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051230/0 /scratch/stefan/7786831/working/building/REAL300025051230 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 87)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/87
`/scratch/stefan/7786831/working/3D/87' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C(=O)CNC2=O)CC1)

`REAL300025051230.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051230.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051230/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051230 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C(=O)CNC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 22, 25, 62, 62, 62, 62, 62, 5, 1, 1, 1, 3, 3, 3, 24, 59, 59, 59, 59, 59, 59, 1, 1, 22, 22, 62, 11, 5, 5, 3, 24, 24, 59, 59, 59, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
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: REAL300025051230 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C(=O)CNC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [41, 25, 13, 1, 1, 1, 1, 1, 1, 1, 41, 41, 57, 62, 62, 62, 62, 136, 201, 201, 201, 201, 201, 201, 62, 62, 25, 25, 1, 41, 57, 57, 62, 136, 136, 201, 201, 201, 62, 62, 62, 62] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 694
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051230 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C(=O)CNC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [131, 131, 131, 159, 165, 201, 201, 201, 201, 201, 68, 59, 43, 42, 6, 42, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 159, 159, 201, 131, 68, 68, 43, 6, 6, 1, 1, 1, 59, 59, 59, 59] 201
rigid atoms, others: [35, 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, 38, 39, 40, 41])
total number of confs: 661
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051230 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051230
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051230/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051230
Building REAL300025051231
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051231'
/scratch/stefan/7786831/working/building/REAL300025051231 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051231

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051231/0 /scratch/stefan/7786831/working/building/REAL300025051231 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 88)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/88
`/scratch/stefan/7786831/working/3D/88' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CC(=O)N(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1=O)

`REAL300025051231.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051231.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051231/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051231 none CN1CC(=O)N(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 19, 19, 19, 9, 2, 2, 2, 1, 1, 1, 5, 10, 10, 10, 34, 52, 124, 124, 124, 124, 124, 1, 1, 19, 19, 19, 19, 19, 19, 19, 9, 9, 2, 5, 5, 10, 34, 34, 124, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 305
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051231 none CN1CC(=O)N(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 19, 19, 19, 19, 33, 52, 52, 52, 102, 133, 201, 201, 201, 201, 201, 19, 19, 1, 1, 2, 2, 2, 1, 1, 5, 5, 19, 33, 33, 52, 102, 102, 201, 19, 19, 19, 19] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 613
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051231 none CN1CC(=O)N(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 169, 124, 124, 124, 124, 109, 75, 75, 29, 75, 13, 1, 1, 1, 1, 1, 1, 1, 124, 124, 201, 201, 201, 201, 201, 201, 201, 169, 169, 124, 109, 109, 75, 29, 29, 1, 124, 124, 124, 124] 201
rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 756
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051231 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051231
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051231/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051231
Building REAL300025051232
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051232'
/scratch/stefan/7786831/working/building/REAL300025051232 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051232

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051232/0 /scratch/stefan/7786831/working/building/REAL300025051232 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 89)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/89
`/scratch/stefan/7786831/working/3D/89' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=CC=CC=C3N2)CC1)

`REAL300025051232.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051232.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051232/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051232 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=CC=CC=C3N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [23, 23, 23, 61, 68, 105, 105, 105, 105, 105, 6, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 61, 61, 105, 23, 6, 6, 3, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1] 110
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 315
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051232 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=CC=CC=C3N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [47, 30, 13, 1, 1, 1, 1, 1, 1, 1, 47, 47, 82, 105, 105, 105, 105, 110, 110, 110, 110, 110, 110, 110, 110, 105, 105, 30, 30, 1, 47, 82, 82, 105, 110, 110, 110, 110, 110, 110, 105, 105, 105, 105] 110
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 400
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051232 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=CC=CC=C3N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [42, 42, 42, 82, 86, 110, 110, 110, 110, 110, 15, 10, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 82, 82, 110, 42, 15, 15, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10] 110
rigid atoms, others: [34, 35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43])
total number of confs: 376
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051232 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051232
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051232/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051232
Building REAL300025051233
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051233'
/scratch/stefan/7786831/working/building/REAL300025051233 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051233

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051233/0 /scratch/stefan/7786831/working/building/REAL300025051233 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 90)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/90
`/scratch/stefan/7786831/working/3D/90' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C)SC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051233.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051233.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051233/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051233 none CC1=C(C)SC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 5, 14, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 7, 29, 29, 29, 90, 110, 196, 196, 196, 196, 196, 1, 1, 5, 5, 5, 5, 5, 5, 5, 2, 7, 7, 29, 90, 90, 196, 1, 1, 1, 1, 5] 201
rigid atoms, others: [38, 39, 8, 9, 10, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 42])
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: REAL300025051233 none CC1=C(C)SC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 5, 14, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 15, 46, 46, 46, 108, 128, 201, 201, 201, 201, 201, 5, 5, 1, 2, 2, 2, 1, 1, 1, 5, 15, 15, 46, 108, 108, 201, 5, 5, 5, 5, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 24, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 586
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051233 none CC1=C(C)SC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 5, 14, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 196, 196, 196, 196, 129, 54, 54, 29, 54, 13, 1, 1, 1, 1, 1, 1, 1, 196, 196, 201, 201, 201, 201, 201, 201, 201, 196, 129, 129, 54, 29, 29, 1, 196, 196, 196, 196, 201] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 749
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051233 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051233
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051233/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051233
Building REAL300025051234
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051234'
/scratch/stefan/7786831/working/building/REAL300025051234 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051234

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051234/0 /scratch/stefan/7786831/working/building/REAL300025051234 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 91)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/91
`/scratch/stefan/7786831/working/3D/91' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2CCCCCC2=O)CC1)

`REAL300025051234.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051234.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051234/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051234 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2CCCCCC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 5, 5, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 44, 47, 109, 109, 109, 109, 109, 4, 1, 1, 1, 3, 3, 3, 21, 36, 36, 36, 36, 36, 36, 36, 1, 1, 44, 44, 109, 18, 4, 4, 3, 21, 21, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 46, 47, 48, 49, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 353
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051234 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2CCCCCC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 5, 5, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 23, 13, 1, 1, 1, 1, 1, 1, 1, 50, 50, 94, 109, 109, 109, 109, 197, 201, 201, 201, 201, 201, 201, 201, 109, 109, 23, 23, 1, 50, 94, 94, 109, 197, 197, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 109, 109, 109, 109] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46, 47, 48, 49])
total number of confs: 821
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051234 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2CCCCCC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 5, 5, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [112, 112, 112, 169, 173, 201, 201, 201, 201, 201, 44, 36, 31, 31, 7, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 169, 169, 201, 112, 44, 44, 31, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 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, 46, 47, 48, 49])
total number of confs: 718
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051234 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051234
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051234/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051234
Building REAL300025051235
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051235'
/scratch/stefan/7786831/working/building/REAL300025051235 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051235

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051235/0 /scratch/stefan/7786831/working/building/REAL300025051235 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 92)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/92
`/scratch/stefan/7786831/working/3D/92' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=C(C)SC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051235.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051235.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051235/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051235 none CCC1=C(C)SC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 5, 14, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 20, 20, 20, 53, 58, 107, 107, 107, 107, 107, 1, 1, 4, 7, 7, 7, 7, 7, 4, 4, 4, 2, 7, 7, 20, 53, 53, 107, 1, 1, 1, 1, 4] 201
rigid atoms, others: [43, 9, 10, 11, 44, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45])
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: REAL300025051235 none CCC1=C(C)SC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 5, 14, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 4, 4, 4, 4, 10, 24, 24, 24, 57, 62, 107, 107, 107, 107, 107, 4, 4, 1, 3, 3, 3, 3, 3, 2, 2, 2, 4, 10, 10, 24, 57, 57, 107, 4, 4, 4, 4, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 45, 25] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 328
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051235 none CCC1=C(C)SC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 5, 14, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 107, 107, 107, 107, 107, 107, 107, 107, 107, 70, 35, 35, 23, 35, 12, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 201, 201, 201, 201, 201, 107, 107, 107, 107, 70, 70, 35, 23, 23, 1, 107, 107, 107, 107, 107] 201
rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45])
total number of confs: 966
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051235 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051235
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051235/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051235
Building REAL300025051236
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051236'
/scratch/stefan/7786831/working/building/REAL300025051236 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051236

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051236/0 /scratch/stefan/7786831/working/building/REAL300025051236 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 93)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/93
`/scratch/stefan/7786831/working/3D/93' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C)=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1)

`REAL300025051236.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051236.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051236/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051236 none CC1=NC(C)=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 6, 23, 23, 23, 53, 59, 124, 124, 124, 124, 124, 1, 1, 7, 7, 7, 7, 7, 7, 7, 2, 6, 6, 23, 53, 53, 124, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 8, 9, 10, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
total number of confs: 327
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051236 none CC1=NC(C)=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 21, 64, 64, 64, 117, 124, 201, 201, 201, 201, 201, 7, 7, 1, 2, 2, 2, 2, 2, 2, 7, 21, 21, 64, 117, 117, 201, 7, 7, 7, 7] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 613
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051236 none CC1=NC(C)=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 124, 124, 124, 124, 79, 41, 41, 24, 41, 12, 1, 1, 1, 1, 1, 1, 1, 124, 124, 201, 201, 201, 201, 201, 201, 201, 124, 79, 79, 41, 24, 24, 1, 124, 124, 124, 124] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41])
total number of confs: 612
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051236 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051236
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051236/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051236
Building REAL300025051237
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051237'
/scratch/stefan/7786831/working/building/REAL300025051237 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051237

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051237/0 /scratch/stefan/7786831/working/building/REAL300025051237 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 94)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/94
`/scratch/stefan/7786831/working/3D/94' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1NC(=O)NC1=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051237.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051237.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051237/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051237 none O=C(CCC1NC(=O)NC1=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 5, 5, 8, 1, 11, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 10, 15, 29, 29, 29, 29, 29, 29, 1, 1, 1, 6, 10, 10, 10, 27, 41, 110, 110, 110, 110, 110, 1, 1, 10, 10, 18, 18, 29, 29, 29, 2, 6, 6, 10, 27, 27, 110, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 42, 11, 12, 13, 44, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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])
total number of confs: 344
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051237 none O=C(CCC1NC(=O)NC1=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 5, 5, 8, 1, 11, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 11, 7, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 44, 58, 58, 58, 109, 134, 201, 201, 201, 201, 201, 29, 29, 11, 11, 7, 7, 1, 1, 1, 29, 44, 44, 58, 109, 109, 201, 29, 29, 29, 29] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 658
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051237 none O=C(CCC1NC(=O)NC1=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 5, 5, 8, 1, 11, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [110, 110, 110, 186, 191, 201, 201, 201, 201, 201, 201, 110, 86, 54, 54, 27, 54, 12, 1, 1, 1, 1, 1, 1, 1, 110, 110, 186, 186, 198, 198, 201, 201, 201, 110, 86, 86, 54, 27, 27, 1, 110, 110, 110, 110] 201
rigid atoms, others: [40, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 891
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051237 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051237
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051237/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051237
Building REAL300025051238
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051238'
/scratch/stefan/7786831/working/building/REAL300025051238 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051238

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051238/0 /scratch/stefan/7786831/working/building/REAL300025051238 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 95)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/95
`/scratch/stefan/7786831/working/3D/95' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)NCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051238.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051238.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051238/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051238 none NC(=O)NCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 191, 136, 136, 136, 136, 105, 69, 69, 31, 69, 13, 1, 1, 1, 1, 1, 1, 1, 136, 136, 201, 201, 201, 201, 201, 191, 191, 136, 105, 105, 69, 31, 31, 1, 136, 136, 136, 136] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41])
total number of confs: 847
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051238 none NC(=O)NCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 15, 15, 10, 2, 2, 2, 1, 1, 1, 4, 8, 8, 8, 30, 50, 136, 136, 136, 136, 136, 1, 1, 15, 15, 15, 15, 15, 10, 10, 2, 4, 4, 8, 30, 30, 136, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 8, 9, 10, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
total number of confs: 333
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051238 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051238
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051238/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051238
Building REAL300025051239
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051239'
/scratch/stefan/7786831/working/building/REAL300025051239 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051239

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051239/0 /scratch/stefan/7786831/working/building/REAL300025051239 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 96)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/96
`/scratch/stefan/7786831/working/3D/96' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C(=O)CCC2=O)CC1)

`REAL300025051239.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051239.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051239/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051239 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C(=O)CCC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 43, 56, 142, 142, 142, 142, 142, 6, 1, 1, 1, 3, 3, 3, 23, 29, 29, 29, 29, 29, 29, 1, 1, 43, 43, 142, 18, 6, 6, 3, 23, 23, 29, 29, 29, 29, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
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: REAL300025051239 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C(=O)CCC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 37, 13, 1, 1, 1, 1, 1, 1, 1, 82, 82, 116, 142, 142, 142, 142, 201, 201, 201, 201, 201, 201, 201, 142, 142, 37, 37, 1, 82, 116, 116, 142, 201, 201, 201, 201, 201, 201, 142, 142, 142, 142] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 819
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051239 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C(=O)CCC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [97, 97, 97, 136, 148, 173, 173, 173, 173, 173, 51, 41, 31, 31, 6, 31, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 136, 136, 173, 97, 51, 51, 31, 6, 6, 1, 1, 1, 1, 41, 41, 41, 41] 173
rigid atoms, others: [35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42])
total number of confs: 597
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051239 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051239
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051239/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051239
Building REAL300025051240
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051240'
/scratch/stefan/7786831/working/building/REAL300025051240 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051240

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051240/0 /scratch/stefan/7786831/working/building/REAL300025051240 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 97)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/97
`/scratch/stefan/7786831/working/3D/97' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)N1C)

`REAL300025051240.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051240.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051240/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051240 none CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 8, 5, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 24, 24, 24, 72, 88, 182, 182, 182, 182, 182, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 24, 72, 72, 182, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4] 201
rigid atoms, others: [37, 6, 7, 8, 39, 40, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 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, 36, 41, 42, 43, 44, 45, 46])
total number of confs: 456
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051240 none CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 8, 5, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 4, 16, 50, 50, 50, 126, 143, 201, 201, 201, 201, 201, 4, 4, 1, 1, 1, 1, 2, 2, 2, 1, 4, 16, 16, 50, 126, 126, 201, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 22, 23, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 647
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051240 none CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 8, 5, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 182, 182, 182, 182, 129, 60, 60, 28, 60, 13, 1, 1, 1, 1, 1, 1, 1, 182, 182, 201, 201, 201, 201, 201, 201, 201, 201, 182, 129, 129, 60, 28, 28, 1, 182, 182, 182, 182, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [36, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 721
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051240 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051240
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051240/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051240
Building REAL300025051241
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051241'
/scratch/stefan/7786831/working/building/REAL300025051241 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051241

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051241/0 /scratch/stefan/7786831/working/building/REAL300025051241 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 98)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/98
`/scratch/stefan/7786831/working/3D/98' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)N1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1)

`REAL300025051241.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051241.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051241/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051241 none NC(=O)N1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 11, 21, 11, 11, 11, 2, 2, 2, 1, 1, 1, 4, 7, 7, 7, 24, 37, 119, 119, 119, 119, 119, 1, 1, 11, 11, 21, 21, 11, 11, 11, 11, 11, 2, 4, 4, 7, 24, 24, 119, 1, 1, 1, 1, 11, 11, 11, 11] 201
rigid atoms, others: [43, 9, 10, 11, 44, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48])
total number of confs: 282
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: REAL300025051241 none NC(=O)N1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 1, 1, 1, 1, 1, 10, 10, 11, 11, 18, 28, 28, 28, 77, 113, 183, 183, 183, 183, 183, 11, 11, 1, 1, 7, 7, 1, 1, 1, 1, 1, 11, 18, 18, 28, 77, 77, 183, 11, 11, 11, 11, 1, 1, 1, 1] 201
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 45, 46, 47, 33, 48, 25, 26, 29, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 514
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051241 none NC(=O)N1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 183, 201, 183, 183, 183, 119, 119, 119, 119, 97, 68, 68, 30, 68, 13, 1, 1, 1, 1, 1, 1, 1, 119, 119, 183, 183, 201, 201, 183, 183, 183, 183, 183, 119, 97, 97, 68, 30, 30, 1, 119, 119, 119, 119, 183, 183, 183, 183] 201
rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 752
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051241 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051241
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051241/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051241
Building REAL300025051242
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051242'
/scratch/stefan/7786831/working/building/REAL300025051242 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051242

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051242/0 /scratch/stefan/7786831/working/building/REAL300025051242 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 99)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/99
`/scratch/stefan/7786831/working/3D/99' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1)

`REAL300025051242.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051242.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051242/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051242 none CC(=O)N1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 12, 20, 12, 12, 12, 2, 2, 2, 1, 1, 1, 6, 12, 12, 12, 33, 46, 118, 118, 118, 118, 118, 1, 1, 12, 12, 20, 20, 20, 12, 12, 12, 12, 12, 2, 6, 6, 12, 33, 33, 118, 1, 1, 1, 1, 12, 12, 12, 12] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49])
total number of confs: 308
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: REAL300025051242 none CC(=O)N1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 11, 11, 12, 12, 21, 35, 35, 35, 80, 108, 177, 177, 177, 177, 177, 12, 12, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 12, 21, 21, 35, 80, 80, 177, 12, 12, 12, 12, 1, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 7, 46, 47, 48, 49, 25, 26, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 503
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051242 none CC(=O)N1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 177, 201, 177, 177, 177, 118, 118, 118, 118, 97, 62, 62, 30, 62, 13, 1, 1, 1, 1, 1, 1, 1, 118, 118, 177, 177, 201, 201, 201, 177, 177, 177, 177, 177, 118, 97, 97, 62, 30, 30, 1, 118, 118, 118, 118, 177, 177, 177, 177] 201
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 763
number of broken/clashed sets: 33
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051242 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051242
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051242/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051242
Building REAL300025051243
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051243'
/scratch/stefan/7786831/working/building/REAL300025051243 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051243

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051243/0 /scratch/stefan/7786831/working/building/REAL300025051243 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 100)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/100
`/scratch/stefan/7786831/working/3D/100' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051243.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051243.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051243/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051243 none CC1=CC=CC=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 20, 20, 12, 2, 2, 2, 1, 1, 1, 6, 12, 12, 12, 38, 53, 122, 122, 122, 122, 122, 1, 1, 20, 20, 20, 20, 20, 20, 20, 12, 12, 2, 6, 6, 12, 38, 38, 122, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
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: REAL300025051243 none CC1=CC=CC=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 20, 20, 20, 20, 39, 47, 47, 47, 88, 115, 201, 201, 201, 201, 201, 20, 20, 2, 2, 2, 1, 1, 1, 1, 5, 5, 20, 39, 39, 47, 88, 88, 201, 20, 20, 20, 20] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 582
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051243 none CC1=CC=CC=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 184, 122, 122, 122, 122, 100, 54, 54, 28, 54, 13, 1, 1, 1, 1, 1, 1, 1, 122, 122, 201, 201, 201, 201, 201, 201, 201, 184, 184, 122, 100, 100, 54, 28, 28, 1, 122, 122, 122, 122] 201
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 802
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051243 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051243
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051243/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051243
Building REAL300025051244
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051244'
/scratch/stefan/7786831/working/building/REAL300025051244 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051244

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051244/0 /scratch/stefan/7786831/working/building/REAL300025051244 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 101)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/101
`/scratch/stefan/7786831/working/3D/101' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CC=CS1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051244.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051244.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051244/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051244 none O=C(CCC1=CC=CS1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 5, 1, 1, 1, 1, 14, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 10, 15, 19, 19, 19, 19, 1, 1, 1, 5, 10, 10, 10, 38, 62, 125, 125, 125, 125, 125, 1, 1, 10, 10, 15, 15, 19, 19, 19, 2, 5, 5, 10, 38, 38, 125, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 359
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051244 none O=C(CCC1=CC=CS1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 5, 1, 1, 1, 1, 14, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 5, 3, 1, 1, 1, 1, 1, 1, 19, 19, 19, 39, 55, 55, 55, 103, 137, 201, 201, 201, 201, 201, 19, 19, 5, 5, 3, 3, 1, 1, 1, 19, 39, 39, 55, 103, 103, 201, 19, 19, 19, 19] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 624
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051244 none O=C(CCC1=CC=CS1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 5, 1, 1, 1, 1, 14, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [125, 125, 125, 189, 195, 201, 201, 201, 201, 125, 105, 62, 62, 28, 62, 13, 1, 1, 1, 1, 1, 1, 1, 125, 125, 189, 189, 195, 195, 201, 201, 201, 125, 105, 105, 62, 28, 28, 1, 125, 125, 125, 125] 201
rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 820
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051244 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051244
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051244/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051244
Building REAL300025051245
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051245'
/scratch/stefan/7786831/working/building/REAL300025051245 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051245

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051245/0 /scratch/stefan/7786831/working/building/REAL300025051245 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 102)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/102
`/scratch/stefan/7786831/working/3D/102' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C=CC=CC2=O)CC1)

`REAL300025051245.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051245.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051245/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051245 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C=CC=CC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 59, 73, 153, 153, 153, 153, 153, 5, 1, 1, 1, 3, 3, 3, 15, 17, 17, 17, 17, 17, 17, 1, 1, 59, 59, 153, 22, 5, 5, 3, 15, 15, 17, 17, 17, 17, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051245 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C=CC=CC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 31, 13, 1, 1, 1, 1, 1, 1, 1, 68, 68, 129, 153, 153, 153, 153, 200, 201, 201, 201, 201, 201, 201, 153, 153, 31, 31, 1, 68, 129, 129, 153, 200, 200, 201, 201, 201, 201, 153, 153, 153, 153] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 830
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051245 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C=CC=CC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 118, 132, 201, 201, 201, 201, 201, 25, 17, 11, 11, 2, 11, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 118, 118, 201, 75, 25, 25, 11, 2, 2, 1, 1, 1, 1, 17, 17, 17, 17] 201
rigid atoms, others: [35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42])
total number of confs: 604
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051245 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051245
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051245/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051245
Building REAL300025051246
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051246'
/scratch/stefan/7786831/working/building/REAL300025051246 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051246

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051246/0 /scratch/stefan/7786831/working/building/REAL300025051246 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 103)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/103
`/scratch/stefan/7786831/working/3D/103' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3CCCC3=C2)CC1)

`REAL300025051246.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051246.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051246/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051246 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3CCCC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 18, 50, 59, 92, 92, 92, 92, 92, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 50, 50, 92, 18, 5, 5, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
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: REAL300025051246 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3CCCC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [54, 27, 13, 1, 1, 1, 1, 1, 1, 1, 54, 54, 82, 92, 92, 92, 92, 201, 201, 201, 201, 201, 201, 201, 201, 92, 92, 27, 27, 1, 54, 82, 82, 92, 201, 201, 201, 201, 201, 201, 201, 201, 201, 92, 92, 92, 92] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46])
total number of confs: 522
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051246 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3CCCC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [65, 65, 65, 152, 169, 201, 201, 201, 201, 201, 17, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 152, 152, 201, 65, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46])
total number of confs: 682
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051246 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051246
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051246/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051246
Building REAL300025051247
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051247'
/scratch/stefan/7786831/working/building/REAL300025051247 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051247

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051247/0 /scratch/stefan/7786831/working/building/REAL300025051247 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 104)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/104
`/scratch/stefan/7786831/working/3D/104' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NOC(C)=C1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051247.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051247.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051247/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051247 none CC1=NOC(C)=C1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 16, 9, 9, 2, 2, 2, 1, 1, 1, 4, 8, 8, 8, 20, 29, 78, 78, 78, 78, 78, 1, 1, 16, 16, 16, 16, 16, 16, 9, 9, 9, 9, 2, 4, 4, 8, 20, 20, 78, 1, 1, 1, 1] 201
rigid atoms, others: [44, 11, 12, 13, 46, 45, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 205
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051247 none CC1=NOC(C)=C1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 16, 16, 16, 36, 55, 55, 55, 99, 129, 201, 201, 201, 201, 201, 16, 16, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 16, 36, 36, 55, 99, 99, 201, 16, 16, 16, 16] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 644
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051247 none CC1=NOC(C)=C1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 127, 127, 78, 78, 78, 78, 65, 43, 43, 25, 43, 12, 1, 1, 1, 1, 1, 1, 1, 78, 78, 201, 201, 201, 201, 201, 201, 127, 127, 127, 127, 78, 65, 65, 43, 25, 25, 1, 78, 78, 78, 78] 201
rigid atoms, others: [43, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47])
total number of confs: 694
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051247 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051247
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051247/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051247
Building REAL300025051248
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051248'
/scratch/stefan/7786831/working/building/REAL300025051248 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051248

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051248/0 /scratch/stefan/7786831/working/building/REAL300025051248 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 105)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/105
`/scratch/stefan/7786831/working/3D/105' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1)

`REAL300025051248.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051248.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051248/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051248 none COCC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
157  conformations in input
total number of sets (complete confs): 157
using faster count positions algorithm for large data
unique positions, atoms: [27, 13, 3, 3, 5, 5, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 8, 16, 69, 69, 69, 69, 69, 1, 1, 5, 5, 27, 27, 27, 13, 13, 5, 5, 2, 5, 5, 5, 8, 8, 69, 1, 1, 1, 1, 5, 5] 157
rigid atoms, others: [43, 9, 10, 11, 44, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46])
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: REAL300025051248 none COCC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
157  conformations in input
total number of sets (complete confs): 157
using faster count positions algorithm for large data
unique positions, atoms: [9, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 11, 11, 11, 11, 16, 34, 112, 112, 112, 112, 112, 5, 5, 1, 1, 10, 10, 10, 4, 4, 1, 1, 5, 11, 11, 11, 16, 16, 112, 5, 5, 5, 5, 1, 1] 157
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 45, 46, 25, 26] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 225
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051248 none COCC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
157  conformations in input
total number of sets (complete confs): 157
using faster count positions algorithm for large data
unique positions, atoms: [157, 157, 94, 94, 112, 112, 69, 69, 69, 69, 54, 53, 53, 35, 53, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 112, 112, 157, 157, 157, 157, 157, 112, 112, 69, 54, 54, 53, 35, 35, 1, 69, 69, 69, 69, 112, 112] 157
rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46])
total number of confs: 700
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051248 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051248
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051248/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051248
Building REAL300025051249
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051249'
/scratch/stefan/7786831/working/building/REAL300025051249 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051249

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051249/0 /scratch/stefan/7786831/working/building/REAL300025051249 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 106)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/106
`/scratch/stefan/7786831/working/3D/106' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(COC1=CC=C(F)C=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051249.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051249.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051249/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051249 none O=C(COC1=CC=C(F)C=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 5, 15, 19, 19, 15, 15, 19, 19, 1, 1, 1, 4, 11, 11, 11, 32, 41, 116, 116, 116, 116, 116, 1, 1, 5, 5, 19, 19, 19, 19, 2, 4, 4, 11, 32, 32, 116, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
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: REAL300025051249 none O=C(COC1=CC=C(F)C=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 35, 68, 68, 68, 118, 140, 201, 201, 201, 201, 201, 19, 19, 8, 8, 1, 1, 1, 1, 19, 35, 35, 68, 118, 118, 201, 19, 19, 19, 19] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 633
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051249 none O=C(COC1=CC=C(F)C=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [116, 116, 116, 142, 201, 201, 201, 201, 201, 201, 201, 116, 91, 68, 68, 46, 68, 13, 1, 1, 1, 1, 1, 1, 1, 116, 116, 142, 142, 201, 201, 201, 201, 116, 91, 91, 68, 46, 46, 1, 116, 116, 116, 116] 201
rigid atoms, others: [39, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 713
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051249 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051249
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051249/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051249
Building REAL300025051250
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051250'
/scratch/stefan/7786831/working/building/REAL300025051250 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051250

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051250/0 /scratch/stefan/7786831/working/building/REAL300025051250 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 107)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/107
`/scratch/stefan/7786831/working/3D/107' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=NNN=C3C=C2)CC1)

`REAL300025051250.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051250.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051250/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051250 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=NNN=C3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 8, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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: [19, 19, 19, 58, 67, 119, 119, 119, 119, 119, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 58, 58, 119, 19, 5, 5, 3, 9, 9, 9, 9, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
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: REAL300025051250 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=NNN=C3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 8, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [54, 26, 13, 1, 1, 1, 1, 1, 1, 1, 54, 54, 97, 119, 119, 119, 119, 201, 201, 201, 201, 201, 201, 201, 201, 119, 119, 26, 26, 1, 54, 97, 97, 119, 201, 201, 201, 201, 119, 119, 119, 119] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 572
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051250 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=NNN=C3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 8, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [63, 63, 63, 146, 159, 201, 201, 201, 201, 201, 17, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 146, 146, 201, 63, 17, 17, 5, 1, 1, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 681
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051250 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051250
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051250/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051250
Building REAL300025051251
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051251'
/scratch/stefan/7786831/working/building/REAL300025051251 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051251

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051251/0 /scratch/stefan/7786831/working/building/REAL300025051251 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 108)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/108
`/scratch/stefan/7786831/working/3D/108' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NNC(C)=C1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051251.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051251.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051251/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051251 none CC1=NNC(C)=C1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 6, 19, 19, 19, 33, 41, 123, 124, 124, 124, 124, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 6, 6, 19, 33, 33, 124, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 46, 45, 48, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
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: REAL300025051251 none CC1=NNC(C)=C1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 13, 14, 14, 14, 30, 50, 50, 50, 105, 134, 201, 201, 201, 201, 201, 14, 14, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 14, 30, 30, 50, 105, 105, 201, 14, 14, 14, 14] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 622
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051251 none CC1=NNC(C)=C1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 124, 124, 124, 124, 83, 47, 47, 26, 47, 12, 1, 1, 1, 1, 1, 1, 1, 124, 124, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 124, 83, 83, 47, 26, 26, 1, 124, 124, 124, 124] 201
rigid atoms, others: [44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48])
total number of confs: 859
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051251 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051251
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051251/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051251
Building REAL300025051252
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051252'
/scratch/stefan/7786831/working/building/REAL300025051252 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051252

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051252/0 /scratch/stefan/7786831/working/building/REAL300025051252 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 109)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/109
`/scratch/stefan/7786831/working/3D/109' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(COCC1=CC=CC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051252.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051252.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051252/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051252 none O=C(COCC1=CC=CC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 4, 9, 18, 29, 29, 24, 29, 29, 1, 1, 1, 3, 6, 6, 6, 24, 33, 76, 76, 76, 76, 76, 1, 1, 4, 4, 18, 18, 29, 29, 29, 29, 29, 2, 3, 3, 6, 24, 24, 76, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 266
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051252 none O=C(COCC1=CC=CC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 23, 10, 3, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 48, 59, 59, 59, 122, 146, 201, 201, 201, 201, 201, 29, 29, 23, 23, 3, 3, 1, 1, 1, 1, 1, 29, 48, 48, 59, 122, 122, 201, 29, 29, 29, 29] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 685
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051252 none O=C(COCC1=CC=CC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 123, 163, 201, 201, 201, 201, 201, 201, 76, 66, 55, 55, 47, 55, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 123, 123, 201, 201, 201, 201, 201, 201, 201, 76, 66, 66, 55, 47, 47, 1, 76, 76, 76, 76] 201
rigid atoms, others: [42, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46])
total number of confs: 834
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051252 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051252
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051252/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051252
Building REAL300025051253
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051253'
/scratch/stefan/7786831/working/building/REAL300025051253 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051253

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051253/0 /scratch/stefan/7786831/working/building/REAL300025051253 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 110)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/110
`/scratch/stefan/7786831/working/3D/110' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1)

`REAL300025051253.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051253.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051253/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051253 none NC(=O)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
191  conformations in input
total number of sets (complete confs): 191
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 3, 5, 5, 2, 2, 2, 1, 1, 1, 4, 19, 19, 19, 67, 82, 147, 147, 147, 147, 147, 1, 1, 5, 5, 5, 5, 5, 5, 2, 4, 4, 19, 67, 67, 147, 1, 1, 1, 1, 5, 5] 191
rigid atoms, others: [38, 39, 40, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43])
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: REAL300025051253 none NC(=O)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
191  conformations in input
total number of sets (complete confs): 191
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 60, 60, 60, 135, 153, 191, 191, 191, 191, 191, 5, 5, 1, 1, 2, 2, 1, 1, 5, 13, 13, 60, 135, 135, 191, 5, 5, 5, 5, 1, 1] 191
rigid atoms, others: [1, 3, 4, 5, 6, 7, 42, 43, 25, 26, 29, 30] set([0, 2, 8, 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])
total number of confs: 626
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051253 none NC(=O)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
191  conformations in input
total number of sets (complete confs): 191
using faster count positions algorithm for large data
unique positions, atoms: [191, 191, 191, 191, 191, 191, 147, 147, 147, 147, 117, 67, 67, 26, 67, 13, 1, 1, 1, 1, 1, 1, 1, 147, 147, 191, 191, 191, 191, 191, 191, 147, 117, 117, 67, 26, 26, 1, 147, 147, 147, 147, 191, 191] 191
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41, 42, 43])
total number of confs: 628
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051253 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051253
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051253/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051253
Building REAL300025051254
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051254'
/scratch/stefan/7786831/working/building/REAL300025051254 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051254

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051254/0 /scratch/stefan/7786831/working/building/REAL300025051254 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 111)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/111
`/scratch/stefan/7786831/working/3D/111' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CC=CC=C1F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051254.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051254.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051254/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051254 none O=C(CCC1=CC=CC=C1F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 10, 12, 15, 15, 15, 15, 15, 15, 1, 1, 1, 4, 9, 9, 9, 27, 40, 113, 113, 113, 113, 113, 1, 1, 10, 10, 12, 12, 15, 15, 15, 15, 2, 4, 4, 9, 27, 27, 113, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 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: REAL300025051254 none O=C(CCC1=CC=CC=C1F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 36, 54, 54, 54, 108, 140, 201, 201, 201, 201, 201, 15, 15, 5, 5, 3, 3, 1, 1, 1, 1, 15, 36, 36, 54, 108, 108, 201, 15, 15, 15, 15] 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, 43, 44, 45])
total number of confs: 664
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051254 none O=C(CCC1=CC=CC=C1F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [113, 113, 113, 196, 199, 201, 201, 201, 201, 201, 201, 113, 96, 55, 55, 27, 55, 13, 1, 1, 1, 1, 1, 1, 1, 113, 113, 196, 196, 199, 199, 201, 201, 201, 201, 113, 96, 96, 55, 27, 27, 1, 113, 113, 113, 113] 201
rigid atoms, others: [41, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 863
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051254 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051254
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051254/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051254
Building REAL300025051255
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051255'
/scratch/stefan/7786831/working/building/REAL300025051255 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051255

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051255/0 /scratch/stefan/7786831/working/building/REAL300025051255 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 112)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/112
`/scratch/stefan/7786831/working/3D/112' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CSC(=O)N1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051255.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051255.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051255/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051255 none CC1=CSC(=O)N1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 14, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 7, 17, 17, 17, 45, 61, 143, 143, 143, 143, 143, 1, 1, 11, 11, 11, 11, 11, 11, 2, 7, 7, 17, 45, 45, 143, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 10, 11, 12, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 348
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051255 none CC1=CSC(=O)N1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 14, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 11, 11, 11, 11, 27, 46, 46, 46, 97, 125, 201, 201, 201, 201, 201, 11, 11, 2, 2, 2, 1, 3, 3, 11, 27, 27, 46, 97, 97, 201, 11, 11, 11, 11] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 593
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051255 none CC1=CSC(=O)N1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 14, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 143, 143, 143, 143, 112, 70, 70, 30, 70, 13, 1, 1, 1, 1, 1, 1, 1, 143, 143, 201, 201, 201, 201, 201, 201, 143, 112, 112, 70, 30, 30, 1, 143, 143, 143, 143] 201
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42])
total number of confs: 819
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051255 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051255
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051255/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051255
Building REAL300025051256
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051256'
/scratch/stefan/7786831/working/building/REAL300025051256 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051256

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051256/0 /scratch/stefan/7786831/working/building/REAL300025051256 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 113)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/113
`/scratch/stefan/7786831/working/3D/113' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCN1N=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051256.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051256.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051256/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051256 none COCCN1N=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 11, 10, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 9, 9, 9, 36, 56, 144, 144, 144, 144, 144, 1, 1, 23, 23, 23, 11, 11, 10, 10, 5, 5, 2, 4, 4, 9, 36, 36, 144, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
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: REAL300025051256 none COCCN1N=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 6, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 18, 18, 18, 61, 92, 178, 178, 178, 178, 178, 5, 5, 16, 16, 16, 6, 6, 5, 5, 1, 1, 5, 10, 10, 18, 61, 61, 178, 5, 5, 5, 5] 201
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 35] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 476
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051256 none COCCN1N=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 200, 178, 178, 178, 178, 178, 144, 144, 144, 144, 122, 75, 75, 29, 75, 13, 1, 1, 1, 1, 1, 1, 1, 144, 144, 201, 201, 201, 201, 201, 200, 200, 178, 178, 144, 122, 122, 75, 29, 29, 1, 144, 144, 144, 144] 201
rigid atoms, others: [42, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46])
total number of confs: 769
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051256 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051256
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051256/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051256
Building REAL300025051257
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051257'
/scratch/stefan/7786831/working/building/REAL300025051257 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051257

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051257/0 /scratch/stefan/7786831/working/building/REAL300025051257 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 114)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/114
`/scratch/stefan/7786831/working/3D/114' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CN=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051257.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051257.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051257/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051257 none CC1=CN=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 2, 9, 9, 2, 2, 2, 1, 1, 1, 4, 18, 18, 18, 59, 74, 140, 140, 140, 140, 140, 1, 1, 9, 9, 9, 9, 9, 9, 2, 4, 4, 18, 59, 59, 140, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051257 none CC1=CN=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 21, 67, 67, 67, 139, 156, 201, 201, 201, 201, 201, 9, 9, 2, 2, 2, 1, 1, 1, 9, 21, 21, 67, 139, 139, 201, 9, 9, 9, 9] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 28, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 658
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051257 none CC1=CN=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 168, 201, 201, 140, 140, 140, 140, 116, 68, 68, 28, 68, 13, 1, 1, 1, 1, 1, 1, 1, 140, 140, 201, 201, 201, 201, 201, 201, 140, 116, 116, 68, 28, 28, 1, 140, 140, 140, 140] 201
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41])
total number of confs: 733
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051257 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051257
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051257/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051257
Building REAL300025051258
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051258'
/scratch/stefan/7786831/working/building/REAL300025051258 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051258

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051258/0 /scratch/stefan/7786831/working/building/REAL300025051258 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 115)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/115
`/scratch/stefan/7786831/working/3D/115' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3C=CNC3=C2)CC1)

`REAL300025051258.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051258.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051258/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051258 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3C=CNC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [21, 21, 21, 61, 71, 102, 102, 102, 102, 102, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 61, 61, 102, 21, 5, 5, 3, 9, 9, 9, 9, 9, 1, 1, 1, 1] 137
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
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: REAL300025051258 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3C=CNC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [63, 31, 13, 1, 1, 1, 1, 1, 1, 1, 63, 63, 86, 102, 102, 102, 102, 137, 137, 137, 137, 137, 137, 137, 137, 102, 102, 31, 31, 1, 63, 86, 86, 102, 137, 137, 137, 137, 137, 102, 102, 102, 102] 137
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 433
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051258 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3C=CNC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [51, 51, 51, 113, 121, 137, 137, 137, 137, 137, 14, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 113, 113, 137, 51, 14, 14, 5, 1, 1, 1, 1, 1, 9, 9, 9, 9] 137
rigid atoms, others: [34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42])
total number of confs: 492
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051258 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051258
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051258/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051258
Building REAL300025051259
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051259'
/scratch/stefan/7786831/working/building/REAL300025051259 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051259

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051259/0 /scratch/stefan/7786831/working/building/REAL300025051259 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 116)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/116
`/scratch/stefan/7786831/working/3D/116' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=CNN=C3N=C2)CC1)

`REAL300025051259.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051259.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051259/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051259 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=CNN=C3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 75, 90, 141, 141, 141, 141, 141, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 75, 75, 141, 24, 5, 5, 3, 9, 9, 9, 9, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
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: REAL300025051259 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=CNN=C3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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: [73, 33, 13, 1, 1, 1, 1, 1, 1, 1, 73, 73, 113, 141, 141, 141, 141, 201, 201, 201, 201, 201, 201, 201, 201, 141, 141, 33, 33, 1, 73, 113, 113, 141, 201, 201, 201, 201, 141, 141, 141, 141] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 616
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051259 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=CNN=C3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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, 152, 169, 201, 201, 201, 201, 201, 15, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 152, 152, 201, 64, 15, 15, 5, 1, 1, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 668
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051259 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051259
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051259/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051259
Building REAL300025051260
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051260'
/scratch/stefan/7786831/working/building/REAL300025051260 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051260

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051260/0 /scratch/stefan/7786831/working/building/REAL300025051260 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 117)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/117
`/scratch/stefan/7786831/working/3D/117' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC2(F)F)CC1)

`REAL300025051260.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051260.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051260/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051260 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC2(F)F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 19, 62, 71, 153, 153, 153, 153, 153, 5, 1, 1, 1, 3, 3, 3, 17, 17, 17, 17, 17, 1, 1, 62, 62, 153, 19, 5, 5, 3, 17, 17, 17, 17, 17, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
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: REAL300025051260 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC2(F)F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [72, 34, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 127, 153, 153, 153, 153, 201, 201, 201, 201, 201, 153, 153, 34, 34, 1, 72, 127, 127, 153, 201, 201, 201, 201, 201, 153, 153, 153, 153] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 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: 766
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051260 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC2(F)F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 149, 158, 201, 201, 201, 201, 201, 25, 17, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 17, 17, 149, 149, 201, 73, 25, 25, 11, 1, 1, 1, 1, 1, 17, 17, 17, 17] 201
rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39])
total number of confs: 673
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051260 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051260
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051260/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051260
Building REAL300025051261
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051261'
/scratch/stefan/7786831/working/building/REAL300025051261 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051261

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051261/0 /scratch/stefan/7786831/working/building/REAL300025051261 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 118)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/118
`/scratch/stefan/7786831/working/3D/118' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NSC=C2)CC1)

`REAL300025051261.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051261.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051261/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051261 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NSC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 14, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 30, 97, 107, 201, 201, 201, 201, 201, 6, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 1, 1, 97, 97, 201, 30, 6, 6, 3, 5, 5, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31])
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: REAL300025051261 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NSC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 14, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [58, 32, 13, 1, 1, 1, 1, 1, 1, 1, 58, 58, 149, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 32, 32, 1, 58, 149, 149, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 25] set([0, 1, 2, 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])
total number of confs: 741
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051261 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NSC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 14, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [45, 45, 45, 125, 133, 201, 201, 201, 201, 201, 10, 5, 4, 4, 1, 4, 1, 1, 1, 1, 1, 5, 5, 125, 125, 201, 45, 10, 10, 4, 1, 1, 5, 5, 5, 5] 201
rigid atoms, others: [14, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35])
total number of confs: 610
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051261 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051261
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051261/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051261
Building REAL300025051262
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051262'
/scratch/stefan/7786831/working/building/REAL300025051262 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051262

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051262/0 /scratch/stefan/7786831/working/building/REAL300025051262 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 119)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/119
`/scratch/stefan/7786831/working/3D/119' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051262.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051262.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051262/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051262 none CCOC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 6, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 6, 18, 18, 18, 61, 93, 190, 190, 190, 190, 190, 1, 1, 3, 14, 14, 14, 14, 14, 3, 2, 6, 6, 18, 61, 61, 190, 1, 1, 1, 1, 3] 201
rigid atoms, others: [39, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43])
total number of confs: 467
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051262 none CCOC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 8, 23, 23, 23, 70, 105, 196, 196, 196, 196, 196, 3, 3, 1, 10, 10, 10, 10, 10, 1, 3, 8, 8, 23, 70, 70, 196, 3, 3, 3, 3, 1] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 43, 25, 31] set([0, 1, 8, 9, 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])
total number of confs: 498
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051262 none CCOC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 198, 196, 196, 196, 196, 190, 190, 190, 190, 149, 73, 73, 32, 73, 13, 1, 1, 1, 1, 1, 1, 1, 190, 190, 196, 201, 201, 201, 201, 201, 196, 190, 149, 149, 73, 32, 32, 1, 190, 190, 190, 190, 196] 201
rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43])
total number of confs: 768
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051262 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051262
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051262/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051262
Building REAL300025051263
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051263'
/scratch/stefan/7786831/working/building/REAL300025051263 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051263

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051263/0 /scratch/stefan/7786831/working/building/REAL300025051263 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 120)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/120
`/scratch/stefan/7786831/working/3D/120' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(F)C=C1F)

`REAL300025051263.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051263.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051263/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051263 none CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(F)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'F', '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, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 15, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 2, 2, 1, 1, 1, 7, 26, 26, 26, 76, 86, 189, 190, 190, 190, 190, 1, 1, 5, 5, 5, 2, 5, 5, 5, 5, 5, 2, 7, 7, 26, 76, 76, 190, 1, 1, 1, 1, 5] 201
rigid atoms, others: [6, 38, 7, 8, 41, 39, 40, 20, 21] set([0, 1, 2, 3, 4, 5, 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, 36, 37, 42])
total number of confs: 491
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051263 none CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(F)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'F', '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, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 15, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 5, 5, 5, 5, 19, 57, 57, 57, 127, 136, 200, 201, 201, 201, 201, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2, 1, 5, 19, 19, 57, 127, 127, 201, 5, 5, 5, 5, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 42, 22, 23, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 632
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051263 none CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(F)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'F', '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, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 15, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 190, 190, 190, 190, 110, 46, 46, 26, 46, 12, 1, 1, 1, 1, 1, 1, 1, 190, 190, 201, 201, 201, 190, 201, 201, 201, 201, 201, 190, 110, 110, 46, 26, 26, 1, 190, 190, 190, 190, 201] 201
rigid atoms, others: [37, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 760
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051263 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051263
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051263/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051263
Building REAL300025051264
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051264'
/scratch/stefan/7786831/working/building/REAL300025051264 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051264

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051264/0 /scratch/stefan/7786831/working/building/REAL300025051264 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 121)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/121
`/scratch/stefan/7786831/working/3D/121' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(COCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1)

`REAL300025051264.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051264.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051264/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051264 none CC1=CC(COCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', '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, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [33, 33, 33, 21, 9, 5, 2, 2, 2, 1, 1, 1, 3, 6, 6, 6, 21, 31, 70, 70, 70, 70, 70, 1, 1, 33, 33, 33, 33, 33, 33, 21, 21, 5, 5, 2, 3, 3, 6, 21, 21, 70, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
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: REAL300025051264 none CC1=CC(COCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', '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, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 7, 15, 23, 33, 33, 33, 33, 50, 59, 59, 59, 124, 152, 201, 201, 201, 201, 201, 33, 33, 1, 1, 2, 2, 2, 1, 7, 7, 23, 23, 33, 50, 50, 59, 124, 124, 201, 33, 33, 33, 33] 201
rigid atoms, others: [0, 1, 2, 3, 4, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 683
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051264 none CC1=CC(COCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', '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, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 194, 149, 118, 70, 70, 70, 70, 62, 53, 53, 42, 53, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 201, 201, 201, 201, 201, 201, 194, 194, 118, 118, 70, 62, 62, 53, 42, 42, 1, 70, 70, 70, 70] 201
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 840
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051264 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051264
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051264/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051264
Building REAL300025051265
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051265'
/scratch/stefan/7786831/working/building/REAL300025051265 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051265

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051265/0 /scratch/stefan/7786831/working/building/REAL300025051265 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 122)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/122
`/scratch/stefan/7786831/working/3D/122' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NOC(COCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051265.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051265.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051265/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051265 none CC1=NOC(COCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 12, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [37, 37, 37, 37, 21, 9, 4, 2, 2, 2, 1, 1, 1, 5, 6, 6, 6, 22, 31, 68, 68, 68, 68, 68, 1, 1, 37, 37, 37, 37, 21, 21, 4, 4, 2, 5, 5, 6, 22, 22, 68, 1, 1, 1, 1, 37] 201
rigid atoms, others: [43, 41, 10, 11, 12, 44, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45])
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: REAL300025051265 none CC1=NOC(COCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 12, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 18, 26, 37, 37, 37, 37, 53, 61, 61, 61, 126, 151, 201, 201, 201, 201, 201, 37, 37, 1, 2, 2, 2, 8, 8, 26, 26, 37, 53, 53, 61, 126, 126, 201, 37, 37, 37, 37, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 45, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 695
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051265 none CC1=NOC(COCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 12, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 181, 137, 105, 68, 68, 68, 68, 62, 55, 55, 40, 55, 13, 1, 1, 1, 1, 1, 1, 1, 68, 68, 201, 201, 201, 201, 181, 181, 105, 105, 68, 62, 62, 55, 40, 40, 1, 68, 68, 68, 68, 201] 201
rigid atoms, others: [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, 37, 38, 39, 41, 42, 43, 44, 45])
total number of confs: 786
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051265 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051265
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051265/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051265
Building REAL300025051266
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051266'
/scratch/stefan/7786831/working/building/REAL300025051266 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051266

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051266/0 /scratch/stefan/7786831/working/building/REAL300025051266 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 123)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/123
`/scratch/stefan/7786831/working/3D/123' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC=C1COCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051266.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051266.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051266/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051266 none CN1N=CC=C1COCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [39, 39, 39, 39, 39, 20, 7, 4, 2, 2, 2, 1, 1, 1, 3, 5, 5, 5, 17, 22, 62, 62, 62, 62, 62, 1, 1, 39, 39, 39, 39, 39, 20, 20, 4, 4, 2, 3, 3, 5, 17, 17, 62, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
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: REAL300025051266 none CN1N=CC=C1COCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 20, 28, 39, 39, 39, 39, 62, 79, 79, 79, 140, 161, 201, 201, 201, 201, 201, 39, 39, 2, 2, 2, 1, 1, 7, 7, 28, 28, 39, 62, 62, 79, 140, 140, 201, 39, 39, 39, 39] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 737
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051266 none CN1N=CC=C1COCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 182, 137, 108, 62, 62, 62, 62, 56, 45, 45, 39, 45, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 201, 201, 201, 201, 201, 182, 182, 108, 108, 62, 56, 56, 45, 39, 39, 1, 62, 62, 62, 62] 201
rigid atoms, others: [42, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46])
total number of confs: 808
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051266 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051266
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051266/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051266
Building REAL300025051267
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051267'
/scratch/stefan/7786831/working/building/REAL300025051267 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051267

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051267/0 /scratch/stefan/7786831/working/building/REAL300025051267 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 124)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/124
`/scratch/stefan/7786831/working/3D/124' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3N=CNC3=N2)CC1)

`REAL300025051267.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051267.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051267/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051267 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3N=CNC3=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 30, 105, 117, 197, 197, 197, 197, 197, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 105, 105, 197, 30, 6, 6, 3, 7, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
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: REAL300025051267 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3N=CNC3=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 34, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 150, 197, 197, 197, 197, 201, 201, 201, 201, 201, 201, 201, 201, 197, 197, 34, 34, 1, 75, 150, 150, 197, 201, 201, 201, 201, 197, 197, 197, 197] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 754
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051267 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3N=CNC3=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [49, 49, 49, 133, 140, 201, 201, 201, 201, 201, 13, 7, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 133, 133, 201, 49, 13, 13, 4, 1, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 619
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051267 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051267/1 /scratch/stefan/7786831/working/building/REAL300025051267 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 125)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/125
`/scratch/stefan/7786831/working/3D/125' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3N=CN=C3N2)CC1)

`REAL300025051267.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051267.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051267/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051267 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3N=CN=C3N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
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, 56, 69, 127, 127, 127, 127, 127, 5, 1, 1, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 56, 56, 127, 18, 5, 5, 3, 17, 17, 17, 17, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 341
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: REAL300025051267 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3N=CN=C3N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [70, 33, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 112, 127, 127, 127, 127, 201, 201, 201, 201, 201, 201, 201, 201, 127, 127, 33, 33, 1, 70, 112, 112, 127, 201, 201, 201, 201, 127, 127, 127, 127] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 597
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051267 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3N=CN=C3N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
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, 154, 167, 201, 201, 201, 201, 201, 26, 17, 11, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 154, 154, 201, 71, 26, 26, 11, 1, 1, 1, 1, 17, 17, 17, 17] 201
rigid atoms, others: [34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 700
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051267 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051267
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051267/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051267/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051267
Building REAL300025051268
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051268'
/scratch/stefan/7786831/working/building/REAL300025051268 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051268

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051268/0 /scratch/stefan/7786831/working/building/REAL300025051268 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 126)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/126
`/scratch/stefan/7786831/working/3D/126' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C)NC(=O)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1)

`REAL300025051268.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051268.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051268/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051268 none CC1=C(C)NC(=O)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 8, 1, 11, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 1, 1, 1, 5, 11, 11, 11, 37, 52, 138, 138, 138, 138, 138, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 2, 5, 5, 11, 37, 37, 138, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 10, 11, 12, 44, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
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: REAL300025051268 none CC1=C(C)NC(=O)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 8, 1, 11, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 24, 39, 39, 39, 104, 130, 201, 201, 201, 201, 201, 10, 10, 1, 2, 2, 2, 2, 2, 2, 1, 10, 24, 24, 39, 104, 104, 201, 10, 10, 10, 10] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 8, 7, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 614
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051268 none CC1=C(C)NC(=O)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 8, 1, 11, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 138, 138, 138, 138, 95, 54, 54, 27, 54, 13, 1, 1, 1, 1, 1, 1, 1, 138, 138, 201, 201, 201, 201, 201, 201, 201, 201, 138, 95, 95, 54, 27, 27, 1, 138, 138, 138, 138] 201
rigid atoms, others: [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, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 636
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051268 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051268
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051268/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051268
Building REAL300025051269
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051269'
/scratch/stefan/7786831/working/building/REAL300025051269 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051269

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051269/0 /scratch/stefan/7786831/working/building/REAL300025051269 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 127)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/127
`/scratch/stefan/7786831/working/3D/127' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=CC=CN3C=N2)CC1)

`REAL300025051269.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051269.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051269/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051269 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=CC=CN3C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 31, 31, 106, 118, 200, 200, 200, 200, 200, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 106, 106, 200, 31, 6, 6, 3, 7, 7, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
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: REAL300025051269 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=CC=CN3C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [68, 31, 13, 1, 1, 1, 1, 1, 1, 1, 68, 68, 148, 200, 200, 200, 200, 201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 31, 31, 1, 68, 148, 148, 200, 201, 201, 201, 201, 201, 200, 200, 200, 200] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 735
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051269 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=CC=CN3C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [46, 46, 46, 121, 132, 201, 201, 201, 201, 201, 11, 7, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 121, 121, 201, 46, 11, 11, 4, 1, 1, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42])
total number of confs: 593
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051269 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051269
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051269/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051269
Building REAL300025051270
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051270'
/scratch/stefan/7786831/working/building/REAL300025051270 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051270

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051270/0 /scratch/stefan/7786831/working/building/REAL300025051270 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 128)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/128
`/scratch/stefan/7786831/working/3D/128' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)S1)

`REAL300025051270.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051270.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051270/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051270 none CC1=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', '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, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 30, 30, 30, 88, 104, 196, 196, 196, 196, 196, 1, 1, 4, 4, 4, 4, 4, 4, 2, 7, 7, 30, 88, 88, 196, 1, 1, 1, 1, 4, 4, 4] 201
rigid atoms, others: [35, 36, 37, 6, 7, 8, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41])
total number of confs: 518
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051270 none CC1=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', '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, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 4, 4, 4, 4, 16, 54, 54, 54, 123, 134, 201, 201, 201, 201, 201, 4, 4, 1, 1, 1, 2, 2, 2, 4, 16, 16, 54, 123, 123, 201, 4, 4, 4, 4, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 22, 23, 24] set([5, 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, 36, 37, 38, 39, 40, 41])
total number of confs: 627
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051270 none CC1=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', '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, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 196, 196, 196, 196, 120, 51, 51, 29, 51, 13, 1, 1, 1, 1, 1, 1, 1, 196, 196, 201, 201, 201, 201, 201, 201, 196, 120, 120, 51, 29, 29, 1, 196, 196, 196, 196, 201, 201, 201] 201
rigid atoms, others: [34, 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, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 732
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051270 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051270
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051270/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051270
Building REAL300025051271
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051271'
/scratch/stefan/7786831/working/building/REAL300025051271 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051271

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051271/0 /scratch/stefan/7786831/working/building/REAL300025051271 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 129)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/129
`/scratch/stefan/7786831/working/3D/129' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCC1)

`REAL300025051271.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051271.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051271/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051271 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 170, 170, 170, 170, 129, 77, 77, 29, 77, 13, 1, 1, 1, 1, 1, 1, 1, 170, 170, 201, 201, 201, 201, 201, 201, 201, 201, 170, 129, 129, 77, 29, 29, 1, 170, 170, 170, 170, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [34, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 838
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051271 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 2, 2, 2, 1, 1, 1, 6, 11, 11, 11, 38, 62, 170, 170, 170, 170, 170, 1, 1, 9, 11, 11, 11, 9, 9, 9, 9, 2, 6, 6, 11, 38, 38, 170, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11] 201
rigid atoms, others: [35, 4, 5, 6, 18, 19, 36, 38, 37] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 373
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051271 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 11, 11, 11, 11, 26, 37, 37, 37, 85, 124, 201, 201, 201, 201, 201, 11, 11, 1, 1, 1, 1, 3, 3, 3, 3, 11, 26, 26, 37, 85, 85, 201, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 39, 40, 41, 42, 43, 44, 45, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 553
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051271 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051271
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051271/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051271
Building REAL300025051272
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051272'
/scratch/stefan/7786831/working/building/REAL300025051272 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051272

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051272/0 /scratch/stefan/7786831/working/building/REAL300025051272 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 130)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/130
`/scratch/stefan/7786831/working/3D/130' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC=CC=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051272.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051272.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051272/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051272 none CCC1=CC=CC=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 20, 20, 12, 20, 20, 12, 2, 2, 2, 1, 1, 1, 5, 9, 9, 9, 30, 41, 95, 95, 95, 95, 95, 1, 1, 20, 20, 20, 20, 20, 20, 12, 20, 20, 12, 12, 2, 5, 5, 9, 30, 30, 95, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 46, 45, 48, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 289
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051272 none CCC1=CC=CC=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 20, 20, 20, 20, 38, 51, 51, 51, 90, 110, 201, 201, 201, 201, 201, 20, 20, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 20, 38, 38, 51, 90, 90, 201, 20, 20, 20, 20] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 34, 35, 33] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 596
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051272 none CCC1=CC=CC=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 181, 201, 201, 181, 95, 95, 95, 95, 83, 51, 51, 27, 51, 13, 1, 1, 1, 1, 1, 1, 1, 95, 95, 201, 201, 201, 201, 201, 201, 181, 201, 201, 181, 181, 95, 83, 83, 51, 27, 27, 1, 95, 95, 95, 95] 201
rigid atoms, others: [44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48])
total number of confs: 873
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051272 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051272
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051272/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051272
Building REAL300025051273
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051273'
/scratch/stefan/7786831/working/building/REAL300025051273 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051273

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051273/0 /scratch/stefan/7786831/working/building/REAL300025051273 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 131)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/131
`/scratch/stefan/7786831/working/3D/131' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2C=CCCC2)CC1)

`REAL300025051273.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051273.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051273/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051273 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2C=CCCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 15, 37, 39, 86, 86, 86, 86, 86, 5, 1, 1, 1, 3, 3, 3, 19, 42, 42, 42, 42, 42, 1, 1, 37, 37, 86, 15, 5, 5, 3, 19, 19, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1] 201
rigid atoms, others: [11, 44, 43, 12, 13, 46, 45, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 353
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051273 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2C=CCCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [39, 25, 13, 1, 1, 1, 1, 1, 1, 1, 39, 39, 71, 86, 86, 86, 86, 190, 201, 201, 201, 201, 201, 86, 86, 25, 25, 1, 39, 71, 71, 86, 190, 190, 201, 201, 201, 201, 201, 201, 201, 201, 201, 86, 86, 86, 86] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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, 45, 46])
total number of confs: 820
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051273 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2C=CCCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [121, 121, 121, 184, 186, 201, 201, 201, 201, 201, 57, 42, 23, 23, 5, 23, 1, 1, 1, 1, 1, 1, 1, 42, 42, 184, 184, 201, 121, 57, 57, 23, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46])
total number of confs: 796
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051273 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051273
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051273/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051273
Building REAL300025051274
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051274'
/scratch/stefan/7786831/working/building/REAL300025051274 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051274

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051274/0 /scratch/stefan/7786831/working/building/REAL300025051274 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 132)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/132
`/scratch/stefan/7786831/working/3D/132' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CC=C(F)C=N2)CC1)

`REAL300025051274.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051274.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051274/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051274 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CC=C(F)C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 15, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 15, 36, 38, 87, 87, 87, 87, 87, 5, 1, 1, 1, 3, 3, 3, 22, 38, 38, 38, 38, 38, 38, 1, 1, 36, 36, 87, 15, 5, 5, 3, 22, 22, 38, 38, 38, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
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: REAL300025051274 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CC=C(F)C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 15, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [41, 26, 13, 1, 1, 1, 1, 1, 1, 1, 41, 41, 76, 87, 87, 87, 87, 189, 201, 201, 201, 201, 201, 201, 87, 87, 26, 26, 1, 41, 76, 76, 87, 189, 189, 201, 201, 201, 87, 87, 87, 87] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 770
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051274 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CC=C(F)C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 15, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [112, 112, 112, 182, 182, 201, 201, 201, 201, 201, 49, 38, 30, 30, 7, 30, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 182, 182, 201, 112, 49, 49, 30, 7, 7, 1, 1, 1, 38, 38, 38, 38] 201
rigid atoms, others: [35, 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, 38, 39, 40, 41])
total number of confs: 781
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051274 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051274
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051274/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051274
Building REAL300025051275
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051275'
/scratch/stefan/7786831/working/building/REAL300025051275 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051275

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051275/0 /scratch/stefan/7786831/working/building/REAL300025051275 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 133)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/133
`/scratch/stefan/7786831/working/3D/133' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC=CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051275.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051275.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051275/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051275 none CCC1=CC=CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 11, 11, 9, 11, 11, 5, 2, 2, 2, 1, 1, 1, 5, 8, 8, 8, 20, 32, 79, 79, 79, 79, 79, 1, 1, 11, 20, 20, 20, 20, 20, 11, 11, 11, 5, 5, 2, 5, 5, 8, 20, 20, 79, 1, 1, 1, 1, 11] 201
rigid atoms, others: [44, 10, 11, 12, 45, 46, 47, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48])
total number of confs: 258
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051275 none CCC1=CC=CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 11, 22, 26, 26, 26, 49, 67, 131, 131, 131, 131, 131, 11, 11, 1, 3, 3, 3, 2, 2, 1, 1, 1, 4, 4, 11, 22, 22, 26, 49, 49, 131, 11, 11, 11, 11, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 48, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 371
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051275 none CCC1=CC=CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 131, 131, 128, 131, 131, 93, 79, 79, 79, 79, 76, 56, 56, 26, 56, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 131, 201, 201, 201, 201, 201, 131, 131, 131, 93, 93, 79, 76, 76, 56, 26, 26, 1, 79, 79, 79, 79, 131] 201
rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48])
total number of confs: 887
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051275 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051275
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051275/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051275
Building REAL300025051276
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051276'
/scratch/stefan/7786831/working/building/REAL300025051276 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051276

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051276/0 /scratch/stefan/7786831/working/building/REAL300025051276 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 134)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/134
`/scratch/stefan/7786831/working/3D/134' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCN3C=NC=C3C2)CC1)

`REAL300025051276.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051276.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051276/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051276 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCN3C=NC=C3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 8, 1, 1, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 23, 23, 65, 83, 158, 158, 158, 158, 158, 5, 1, 1, 1, 3, 3, 3, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 65, 65, 158, 23, 5, 5, 3, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 407
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051276 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCN3C=NC=C3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 8, 1, 1, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [82, 35, 13, 1, 1, 1, 1, 1, 1, 1, 82, 82, 133, 158, 158, 158, 158, 201, 201, 201, 201, 201, 201, 201, 201, 158, 158, 35, 35, 1, 82, 133, 133, 158, 201, 201, 201, 201, 201, 201, 201, 201, 201, 158, 158, 158, 158] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46])
total number of confs: 730
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051276 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCN3C=NC=C3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 8, 1, 1, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [79, 79, 79, 144, 160, 201, 201, 201, 201, 201, 24, 16, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 144, 144, 201, 79, 24, 24, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46])
total number of confs: 651
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051276 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051276
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051276/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051276
Building REAL300025051277
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051277'
/scratch/stefan/7786831/working/building/REAL300025051277 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051277

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051277/0 /scratch/stefan/7786831/working/building/REAL300025051277 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 135)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/135
`/scratch/stefan/7786831/working/3D/135' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CC(F)(F)C2)CC1)

`REAL300025051277.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051277.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051277/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051277 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CC(F)(F)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', '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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 12, 19, 24, 63, 63, 63, 63, 63, 5, 1, 1, 1, 3, 3, 3, 18, 44, 44, 44, 44, 44, 1, 1, 19, 19, 63, 12, 5, 5, 3, 18, 18, 44, 44, 44, 44, 44, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 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: REAL300025051277 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CC(F)(F)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', '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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [43, 28, 13, 1, 1, 1, 1, 1, 1, 1, 43, 43, 60, 63, 63, 63, 63, 175, 201, 201, 201, 201, 201, 63, 63, 28, 28, 1, 43, 60, 60, 63, 175, 175, 201, 201, 201, 201, 201, 63, 63, 63, 63] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 823
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051277 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CC(F)(F)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', '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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [93, 93, 93, 125, 149, 201, 201, 201, 201, 201, 51, 44, 27, 27, 6, 27, 1, 1, 1, 1, 1, 1, 1, 44, 44, 125, 125, 201, 93, 51, 51, 27, 6, 6, 1, 1, 1, 1, 1, 44, 44, 44, 44] 201
rigid atoms, others: [34, 35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42])
total number of confs: 648
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051277 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051277
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051277/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051277
Building REAL300025051278
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051278'
/scratch/stefan/7786831/working/building/REAL300025051278 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051278

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051278/0 /scratch/stefan/7786831/working/building/REAL300025051278 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 136)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/136
`/scratch/stefan/7786831/working/3D/136' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC1=NN(C)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051278.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051278.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051278/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051278 none COCC1=NN(C)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 18, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 4, 6, 6, 6, 24, 36, 89, 89, 89, 89, 89, 1, 1, 29, 29, 29, 18, 18, 9, 9, 9, 9, 2, 4, 4, 6, 24, 24, 89, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
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: REAL300025051278 none COCC1=NN(C)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 4, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 16, 24, 24, 24, 79, 104, 171, 171, 171, 171, 171, 9, 9, 16, 16, 16, 4, 4, 2, 2, 2, 1, 9, 16, 16, 24, 79, 79, 171, 9, 9, 9, 9] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 35] 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, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 513
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051278 none COCC1=NN(C)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 171, 171, 171, 171, 171, 171, 89, 89, 89, 89, 77, 52, 52, 26, 52, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 201, 201, 201, 201, 201, 171, 171, 171, 171, 89, 77, 77, 52, 26, 26, 1, 89, 89, 89, 89] 201
rigid atoms, others: [42, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46])
total number of confs: 643
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051278 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051278
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051278/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051278
Building REAL300025051279
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051279'
/scratch/stefan/7786831/working/building/REAL300025051279 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051279

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051279/0 /scratch/stefan/7786831/working/building/REAL300025051279 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 137)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/137
`/scratch/stefan/7786831/working/3D/137' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=NN=C(C)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051279.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051279.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051279/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051279 none CCC1=NN=C(C)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 4, 9, 9, 9, 25, 38, 123, 123, 123, 123, 123, 1, 1, 18, 18, 18, 18, 18, 9, 9, 9, 9, 2, 4, 4, 9, 25, 25, 123, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
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: REAL300025051279 none CCC1=NN=C(C)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 19, 31, 31, 31, 67, 97, 182, 182, 182, 182, 182, 9, 9, 6, 6, 6, 6, 6, 2, 2, 2, 1, 9, 19, 19, 31, 67, 67, 182, 9, 9, 9, 9] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 35] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 503
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051279 none CCC1=NN=C(C)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 182, 182, 182, 182, 182, 182, 182, 123, 123, 123, 123, 100, 60, 60, 31, 60, 13, 1, 1, 1, 1, 1, 1, 1, 123, 123, 201, 201, 201, 201, 201, 182, 182, 182, 182, 123, 100, 100, 60, 31, 31, 1, 123, 123, 123, 123] 201
rigid atoms, others: [42, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46])
total number of confs: 717
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051279 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051279
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051279/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051279
Building REAL300025051280
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051280'
/scratch/stefan/7786831/working/building/REAL300025051280 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051280

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051280/0 /scratch/stefan/7786831/working/building/REAL300025051280 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 138)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/138
`/scratch/stefan/7786831/working/3D/138' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3C=CC2O3)CC1)

`REAL300025051280.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051280.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051280/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051280 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3C=CC2O3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 29, 93, 108, 194, 194, 194, 194, 194, 6, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 13, 1, 1, 93, 93, 194, 29, 6, 6, 3, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 532
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051280 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3C=CC2O3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 36, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 162, 194, 194, 194, 194, 201, 201, 201, 201, 201, 201, 194, 194, 36, 36, 1, 75, 162, 162, 194, 201, 201, 201, 201, 201, 201, 201, 194, 194, 194, 194] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 757
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051280 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3C=CC2O3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 61, 61, 136, 150, 201, 201, 201, 201, 201, 19, 13, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 13, 13, 136, 136, 201, 61, 19, 19, 9, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42])
total number of confs: 625
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051280 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051280
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051280/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051280
Building REAL300025051281
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051281'
/scratch/stefan/7786831/working/building/REAL300025051281 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051281

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051281/0 /scratch/stefan/7786831/working/building/REAL300025051281 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 139)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/139
`/scratch/stefan/7786831/working/3D/139' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3=NC=CN3C2)CC1)

`REAL300025051281.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051281.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051281/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051281 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3=NC=CN3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 1, 1, 8, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 80, 94, 158, 158, 158, 158, 158, 5, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 80, 80, 158, 24, 5, 5, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 447
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051281 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3=NC=CN3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 1, 1, 8, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [72, 32, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 125, 158, 158, 158, 158, 201, 201, 201, 201, 201, 201, 201, 201, 158, 158, 32, 32, 1, 72, 125, 125, 158, 201, 201, 201, 201, 201, 201, 201, 201, 201, 158, 158, 158, 158] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46])
total number of confs: 740
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051281 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3=NC=CN3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 1, 1, 8, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [76, 76, 76, 153, 164, 201, 201, 201, 201, 201, 25, 14, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 153, 153, 201, 76, 25, 25, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46])
total number of confs: 697
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051281 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051281
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051281/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051281
Building REAL300025051282
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051282'
/scratch/stefan/7786831/working/building/REAL300025051282 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051282

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051282/0 /scratch/stefan/7786831/working/building/REAL300025051282 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 140)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/140
`/scratch/stefan/7786831/working/3D/140' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCN3C=CN=C3C2)CC1)

`REAL300025051282.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051282.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051282/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051282 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCN3C=CN=C3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
168  conformations in input
total number of sets (complete confs): 168
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 64, 78, 147, 147, 147, 147, 147, 5, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 64, 64, 147, 22, 5, 5, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1] 168
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 394
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051282 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCN3C=CN=C3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
168  conformations in input
total number of sets (complete confs): 168
using faster count positions algorithm for large data
unique positions, atoms: [77, 34, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 124, 147, 147, 147, 147, 168, 168, 168, 168, 168, 168, 168, 168, 147, 147, 34, 34, 1, 77, 124, 124, 147, 168, 168, 168, 168, 168, 168, 168, 168, 168, 147, 147, 147, 147] 168
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46])
total number of confs: 627
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051282 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCN3C=CN=C3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
168  conformations in input
total number of sets (complete confs): 168
using faster count positions algorithm for large data
unique positions, atoms: [61, 61, 61, 114, 129, 168, 168, 168, 168, 168, 21, 15, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 114, 114, 168, 61, 21, 21, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15] 168
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46])
total number of confs: 529
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051282 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051282
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051282/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051282
Building REAL300025051283
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051283'
/scratch/stefan/7786831/working/building/REAL300025051283 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051283

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051283/0 /scratch/stefan/7786831/working/building/REAL300025051283 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 141)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/141
`/scratch/stefan/7786831/working/3D/141' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3=CN=CN3C2)CC1)

`REAL300025051283.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051283.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051283/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051283 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3=CN=CN3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 8, 1, 8, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 77, 93, 155, 155, 155, 155, 155, 5, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 77, 77, 155, 24, 5, 5, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
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: REAL300025051283 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3=CN=CN3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 8, 1, 8, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [69, 33, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 128, 155, 155, 155, 155, 201, 201, 201, 201, 201, 201, 201, 201, 155, 155, 33, 33, 1, 69, 128, 128, 155, 201, 201, 201, 201, 201, 201, 201, 201, 201, 155, 155, 155, 155] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46])
total number of confs: 738
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051283 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3=CN=CN3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 8, 1, 8, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [79, 79, 79, 151, 163, 201, 201, 201, 201, 201, 24, 14, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 151, 151, 201, 79, 24, 24, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46])
total number of confs: 684
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051283 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051283
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051283/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051283
Building REAL300025051284
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051284'
/scratch/stefan/7786831/working/building/REAL300025051284 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051284

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051284/0 /scratch/stefan/7786831/working/building/REAL300025051284 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 142)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/142
`/scratch/stefan/7786831/working/3D/142' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1CCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051284.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051284.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051284/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051284 none COC1CCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 6, 6, 6, 6, 6, 2, 2, 2, 1, 1, 1, 7, 20, 20, 20, 71, 93, 193, 193, 193, 193, 193, 1, 1, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 2, 7, 7, 20, 71, 71, 193, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 46, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 482
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051284 none COC1CCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 16, 32, 32, 32, 95, 121, 201, 201, 201, 201, 201, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 16, 16, 32, 95, 95, 201, 6, 6, 6, 6] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 35, 28, 29, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 569
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051284 none COC1CCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 193, 193, 193, 193, 148, 74, 74, 30, 74, 13, 1, 1, 1, 1, 1, 1, 1, 193, 193, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 193, 148, 148, 74, 30, 30, 1, 193, 193, 193, 193] 201
rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46])
total number of confs: 771
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051284 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051284
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051284/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051284
Building REAL300025051285
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051285'
/scratch/stefan/7786831/working/building/REAL300025051285 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051285

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051285/0 /scratch/stefan/7786831/working/building/REAL300025051285 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 143)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/143
`/scratch/stefan/7786831/working/3D/143' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CO1)

`REAL300025051285.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051285.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051285/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051285 none CC1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 2, 2, 2, 1, 1, 1, 6, 20, 20, 20, 50, 62, 141, 141, 141, 141, 141, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 6, 6, 20, 50, 50, 141, 1, 1, 1, 1, 7, 7] 201
rigid atoms, others: [6, 38, 7, 8, 41, 39, 40, 20, 21] set([0, 1, 2, 3, 4, 5, 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, 36, 37, 42, 43])
total number of confs: 356
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051285 none CC1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 7, 25, 62, 62, 62, 112, 127, 201, 201, 201, 201, 201, 7, 7, 1, 1, 2, 2, 2, 1, 1, 1, 1, 7, 25, 25, 62, 112, 112, 201, 7, 7, 7, 7, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 42, 43, 22, 23, 27, 28, 29, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 615
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051285 none CC1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 141, 141, 141, 107, 51, 51, 29, 51, 12, 1, 1, 1, 1, 1, 1, 1, 141, 141, 201, 201, 201, 201, 201, 201, 201, 201, 201, 141, 107, 107, 51, 29, 29, 1, 141, 141, 141, 141, 201, 201] 201
rigid atoms, others: [37, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43])
total number of confs: 746
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051285 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051285
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051285/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051285
Building REAL300025051286
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051286'
/scratch/stefan/7786831/working/building/REAL300025051286 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051286

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051286/0 /scratch/stefan/7786831/working/building/REAL300025051286 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 144)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/144
`/scratch/stefan/7786831/working/3D/144' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCC3CC32)CC1)

`REAL300025051286.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051286.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051286/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051286 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCC3CC32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 17, 51, 62, 130, 130, 130, 130, 130, 5, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 1, 1, 51, 51, 130, 17, 5, 5, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1] 201
rigid atoms, others: [11, 44, 43, 12, 13, 46, 45, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
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: REAL300025051286 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCC3CC32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [59, 29, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 111, 130, 130, 130, 130, 201, 201, 201, 201, 201, 201, 130, 130, 29, 29, 1, 59, 111, 111, 130, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 130, 130, 130, 130] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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, 45, 46])
total number of confs: 750
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051286 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCC3CC32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [65, 65, 65, 136, 152, 201, 201, 201, 201, 201, 21, 14, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 14, 136, 136, 201, 65, 21, 21, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 43, 44, 45, 46])
total number of confs: 663
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051286 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051286
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051286/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051286
Building REAL300025051287
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051287'
/scratch/stefan/7786831/working/building/REAL300025051287 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051287

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051287/0 /scratch/stefan/7786831/working/building/REAL300025051287 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 145)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/145
`/scratch/stefan/7786831/working/3D/145' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCC3CC32)CC1)

`REAL300025051287.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051287.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051287/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051287 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCC3CC32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 24, 30, 77, 77, 77, 77, 77, 5, 1, 1, 1, 3, 3, 3, 21, 42, 42, 42, 42, 42, 1, 1, 24, 24, 77, 11, 5, 5, 3, 21, 21, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1] 201
rigid atoms, others: [11, 44, 43, 12, 13, 46, 45, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 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.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051287 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCC3CC32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [49, 29, 13, 1, 1, 1, 1, 1, 1, 1, 49, 49, 71, 77, 77, 77, 77, 189, 201, 201, 201, 201, 201, 77, 77, 29, 29, 1, 49, 71, 71, 77, 189, 189, 201, 201, 201, 201, 201, 201, 201, 201, 201, 77, 77, 77, 77] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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, 45, 46])
total number of confs: 815
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051287 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCC3CC32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [95, 95, 95, 138, 160, 201, 201, 201, 201, 201, 49, 42, 27, 27, 6, 27, 1, 1, 1, 1, 1, 1, 1, 42, 42, 138, 138, 201, 95, 49, 49, 27, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46])
total number of confs: 687
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051287 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051287
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051287/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051287
Building REAL300025051288
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051288'
/scratch/stefan/7786831/working/building/REAL300025051288 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051288

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051288/0 /scratch/stefan/7786831/working/building/REAL300025051288 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 146)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/146
`/scratch/stefan/7786831/working/3D/146' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3CC3C2)CC1)

`REAL300025051288.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051288.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051288/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051288 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3CC3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 17, 53, 63, 128, 128, 128, 128, 128, 5, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 1, 1, 53, 53, 128, 17, 5, 5, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1] 201
rigid atoms, others: [11, 44, 43, 12, 13, 46, 45, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 339
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051288 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3CC3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [63, 28, 13, 1, 1, 1, 1, 1, 1, 1, 63, 63, 115, 128, 128, 128, 128, 201, 201, 201, 201, 201, 201, 128, 128, 28, 28, 1, 63, 115, 115, 128, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 128, 128, 128, 128] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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, 45, 46])
total number of confs: 730
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051288 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3CC3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [70, 70, 70, 146, 157, 201, 201, 201, 201, 201, 21, 15, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 15, 15, 146, 146, 201, 70, 21, 21, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 43, 44, 45, 46])
total number of confs: 666
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051288 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051288
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051288/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051288
Building REAL300025051289
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051289'
/scratch/stefan/7786831/working/building/REAL300025051289 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051289

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051289/0 /scratch/stefan/7786831/working/building/REAL300025051289 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 147)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/147
`/scratch/stefan/7786831/working/3D/147' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)C(OC)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051289.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051289.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051289/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051289 none CCC(C)C(OC)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 163, 201, 152, 163, 163, 152, 152, 152, 110, 63, 63, 30, 63, 13, 1, 1, 1, 1, 1, 1, 1, 152, 152, 201, 201, 201, 201, 201, 201, 201, 201, 201, 163, 163, 163, 163, 152, 110, 110, 63, 30, 30, 1, 152, 152, 152, 152] 201
rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48])
total number of confs: 855
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051289 none CCC(C)C(OC)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 9, 4, 9, 2, 4, 4, 2, 2, 1, 1, 1, 6, 13, 13, 13, 42, 54, 152, 152, 152, 152, 152, 1, 1, 13, 13, 13, 13, 13, 9, 9, 9, 9, 4, 4, 4, 4, 2, 6, 6, 13, 42, 42, 152, 1, 1, 1, 1] 201
rigid atoms, others: [9, 10, 11, 45, 46, 47, 48, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 381
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051289 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051289
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051289/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051289
Building REAL300025051290
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051290'
/scratch/stefan/7786831/working/building/REAL300025051290 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051290

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051290/0 /scratch/stefan/7786831/working/building/REAL300025051290 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 148)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/148
`/scratch/stefan/7786831/working/3D/148' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025051290.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051290.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051290/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051290 none COC1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 8, 8, 8, 8, 2, 2, 2, 1, 1, 1, 4, 10, 10, 10, 30, 50, 143, 143, 143, 143, 143, 1, 1, 8, 17, 17, 17, 8, 8, 8, 8, 8, 8, 2, 4, 4, 10, 30, 30, 143, 1, 1, 1, 1, 8, 8] 201
rigid atoms, others: [43, 8, 9, 10, 23, 44, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 45, 46])
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: REAL300025051290 none COC1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 18, 32, 32, 32, 80, 122, 201, 201, 201, 201, 201, 8, 8, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 8, 18, 18, 32, 80, 80, 201, 8, 8, 8, 8, 1, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 45, 46, 24, 28, 29, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 536
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051290 none COC1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 143, 143, 143, 143, 117, 66, 66, 30, 66, 13, 1, 1, 1, 1, 1, 1, 1, 143, 143, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 143, 117, 117, 66, 30, 30, 1, 143, 143, 143, 143, 201, 201] 201
rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46])
total number of confs: 783
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051290 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051290
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051290/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051290
Building REAL300025051291
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051291'
/scratch/stefan/7786831/working/building/REAL300025051291 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051291

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051291/0 /scratch/stefan/7786831/working/building/REAL300025051291 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 149)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/149
`/scratch/stefan/7786831/working/3D/149' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CCN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1=O)

`REAL300025051291.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051291.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051291/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051291 none CN1CCN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 6, 2, 2, 2, 1, 1, 1, 7, 30, 30, 30, 90, 102, 182, 182, 182, 182, 182, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 2, 7, 7, 30, 90, 90, 182, 1, 1, 1, 1, 8, 8] 201
rigid atoms, others: [8, 9, 10, 43, 44, 45, 46, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 47, 48])
total number of confs: 499
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051291 none CN1CCN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations 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, 8, 8, 8, 8, 16, 47, 47, 47, 116, 127, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 5, 5, 8, 16, 16, 47, 116, 116, 201, 8, 8, 8, 8, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 47, 48, 24, 25, 26, 5, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 600
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051291 none CN1CCN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations 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, 182, 182, 182, 182, 166, 75, 75, 35, 75, 13, 1, 1, 1, 1, 1, 1, 1, 182, 182, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 182, 166, 166, 75, 35, 35, 1, 182, 182, 182, 182, 201, 201] 201
rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48])
total number of confs: 809
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051291 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051291
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051291/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051291
Building REAL300025051292
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051292'
/scratch/stefan/7786831/working/building/REAL300025051292 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051292

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051292/0 /scratch/stefan/7786831/working/building/REAL300025051292 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 150)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/150
`/scratch/stefan/7786831/working/3D/150' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C=C(C3CC3)C=N2)CC1)

`REAL300025051292.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051292.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051292/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051292 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C=C(C3CC3)C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 1, 1, 5, 5, 5, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 12, 25, 25, 43, 43, 43, 43, 43, 4, 1, 1, 1, 3, 3, 3, 14, 29, 29, 29, 57, 57, 29, 29, 1, 1, 25, 25, 43, 12, 4, 4, 3, 14, 14, 29, 57, 57, 57, 57, 57, 29, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
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: REAL300025051292 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C=C(C3CC3)C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 1, 1, 5, 5, 5, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 16, 13, 1, 1, 1, 1, 1, 1, 1, 21, 21, 42, 43, 43, 43, 43, 95, 124, 124, 124, 201, 201, 124, 124, 43, 43, 16, 16, 1, 21, 42, 42, 43, 95, 95, 124, 201, 201, 201, 201, 201, 124, 43, 43, 43, 43] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46])
total number of confs: 721
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051292 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C=C(C3CC3)C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 1, 1, 5, 5, 5, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [143, 143, 143, 197, 197, 201, 201, 201, 201, 201, 74, 57, 52, 52, 16, 52, 8, 8, 8, 1, 1, 1, 1, 8, 8, 57, 57, 197, 197, 201, 143, 74, 74, 52, 16, 16, 8, 1, 1, 1, 1, 1, 8, 57, 57, 57, 57] 201
rigid atoms, others: [37, 38, 39, 40, 41, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46])
total number of confs: 795
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051292 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C=C(C3CC3)C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 1, 1, 5, 5, 5, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [74, 74, 74, 109, 109, 124, 124, 124, 124, 124, 37, 29, 25, 25, 5, 25, 1, 1, 1, 1, 1, 8, 8, 1, 1, 29, 29, 109, 109, 124, 74, 37, 37, 25, 5, 5, 1, 8, 8, 8, 8, 8, 1, 29, 29, 29, 29] 201
rigid atoms, others: [36, 42, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 43, 44, 45, 46])
total number of confs: 483
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051292 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051292
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051292/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051292
Building REAL300025051293
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051293'
/scratch/stefan/7786831/working/building/REAL300025051293 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051293

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051293/0 /scratch/stefan/7786831/working/building/REAL300025051293 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 151)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/151
`/scratch/stefan/7786831/working/3D/151' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC1CCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051293.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051293.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051293/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051293 none CCCC1CCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 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.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 20, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 4, 9, 9, 9, 29, 42, 92, 92, 92, 92, 92, 1, 1, 21, 21, 21, 21, 21, 20, 20, 9, 9, 9, 9, 9, 9, 9, 9, 2, 4, 4, 9, 29, 29, 92, 1, 1, 1, 1] 201
rigid atoms, others: [10, 11, 12, 48, 49, 50, 51, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 283
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051293 none CCCC1CCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 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.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 5, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 19, 37, 37, 37, 75, 101, 161, 161, 161, 161, 161, 9, 9, 6, 6, 6, 6, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 9, 19, 19, 37, 75, 75, 161, 9, 9, 9, 9] 201
rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 39, 34, 40, 35, 36, 38, 37] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 482
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051293 none CCCC1CCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 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.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 161, 161, 161, 161, 161, 92, 92, 92, 92, 80, 55, 55, 26, 55, 13, 1, 1, 1, 1, 1, 1, 1, 92, 92, 201, 201, 201, 201, 201, 201, 201, 161, 161, 161, 161, 161, 161, 161, 161, 92, 80, 80, 55, 26, 26, 1, 92, 92, 92, 92] 201
rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51])
total number of confs: 790
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051293 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051293
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051293/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051293
Building REAL300025051294
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051294'
/scratch/stefan/7786831/working/building/REAL300025051294 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051294

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051294/0 /scratch/stefan/7786831/working/building/REAL300025051294 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 152)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/152
`/scratch/stefan/7786831/working/3D/152' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CC)C(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051294.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051294.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051294/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051294 none CCC(CC)C(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 157, 155, 154, 201, 92, 155, 92, 92, 92, 81, 58, 58, 25, 58, 13, 1, 1, 1, 1, 1, 1, 1, 92, 92, 201, 201, 201, 200, 201, 158, 197, 201, 201, 201, 201, 155, 155, 155, 155, 92, 81, 81, 58, 25, 25, 1, 92, 92, 92, 92] 201
rigid atoms, others: [46, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50])
total number of confs: 1194
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: REAL300025051294 none CCC(CC)C(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 12, 9, 13, 18, 2, 9, 2, 2, 1, 1, 1, 4, 8, 8, 8, 23, 35, 92, 92, 92, 92, 92, 1, 1, 18, 18, 18, 16, 18, 14, 17, 18, 18, 18, 18, 9, 9, 9, 9, 2, 4, 4, 8, 23, 23, 92, 1, 1, 1, 1] 201
rigid atoms, others: [9, 10, 11, 47, 48, 49, 50, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 299
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051294 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051294
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051294/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051294
Building REAL300025051295
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051295'
/scratch/stefan/7786831/working/building/REAL300025051295 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051295

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051295/0 /scratch/stefan/7786831/working/building/REAL300025051295 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 153)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/153
`/scratch/stefan/7786831/working/3D/153' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CS(=O)(=O)C2)CC1)

`REAL300025051295.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051295.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051295/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051295 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CS(=O)(=O)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 14, 11, 11, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 30, 37, 85, 85, 85, 85, 85, 5, 1, 1, 1, 3, 3, 3, 16, 42, 42, 42, 42, 42, 1, 1, 30, 30, 85, 13, 5, 5, 3, 16, 16, 42, 42, 42, 42, 42, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 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: REAL300025051295 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CS(=O)(=O)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 14, 11, 11, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [54, 32, 13, 1, 1, 1, 1, 1, 1, 1, 54, 54, 78, 85, 85, 85, 85, 172, 201, 201, 201, 201, 201, 85, 85, 32, 32, 1, 54, 78, 78, 85, 172, 172, 201, 201, 201, 201, 201, 85, 85, 85, 85] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 854
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051295 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CS(=O)(=O)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 14, 11, 11, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
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, 130, 146, 201, 201, 201, 201, 201, 50, 42, 27, 27, 6, 27, 1, 1, 1, 1, 1, 1, 1, 42, 42, 130, 130, 201, 97, 50, 50, 27, 6, 6, 1, 1, 1, 1, 1, 42, 42, 42, 42] 201
rigid atoms, others: [34, 35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42])
total number of confs: 638
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051295 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051295
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051295/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051295
Building REAL300025051296
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051296'
/scratch/stefan/7786831/working/building/REAL300025051296 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051296

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051296/0 /scratch/stefan/7786831/working/building/REAL300025051296 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 154)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/154
`/scratch/stefan/7786831/working/3D/154' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=NN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1=O)

`REAL300025051296.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051296.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051296/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051296 none CN1C=NN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 18, 9, 2, 2, 2, 1, 1, 1, 6, 10, 10, 10, 41, 60, 142, 142, 142, 142, 142, 1, 1, 18, 18, 18, 18, 18, 18, 9, 9, 2, 6, 6, 10, 41, 41, 142, 1, 1, 1, 1] 201
rigid atoms, others: [39, 8, 9, 10, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 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: REAL300025051296 none CN1C=NN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 18, 18, 35, 44, 44, 44, 95, 128, 201, 201, 201, 201, 201, 18, 18, 1, 1, 2, 2, 2, 1, 5, 5, 18, 35, 35, 44, 95, 95, 201, 18, 18, 18, 18] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 591
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051296 none CN1C=NN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 187, 142, 142, 142, 142, 127, 89, 89, 31, 89, 13, 1, 1, 1, 1, 1, 1, 1, 142, 142, 201, 201, 201, 201, 201, 201, 187, 187, 142, 127, 127, 89, 31, 31, 1, 142, 142, 142, 142] 201
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42])
total number of confs: 772
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051296 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051296
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051296/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051296
Building REAL300025051297
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051297'
/scratch/stefan/7786831/working/building/REAL300025051297 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051297

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051297/0 /scratch/stefan/7786831/working/building/REAL300025051297 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 155)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/155
`/scratch/stefan/7786831/working/3D/155' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(C3CC3)=NN2)CC1)

`REAL300025051297.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051297.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051297/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051297 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(C3CC3)=NN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 15, 37, 44, 96, 96, 96, 96, 96, 5, 1, 1, 1, 3, 3, 3, 11, 11, 11, 54, 54, 11, 11, 1, 1, 37, 37, 96, 15, 5, 5, 3, 11, 54, 54, 54, 54, 54, 11, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 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: REAL300025051297 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(C3CC3)=NN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [49, 28, 13, 1, 1, 1, 1, 1, 1, 1, 49, 49, 76, 96, 96, 96, 96, 134, 134, 134, 201, 201, 134, 134, 96, 96, 28, 28, 1, 49, 76, 76, 96, 134, 201, 201, 201, 201, 201, 134, 96, 96, 96, 96] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 723
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051297 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(C3CC3)=NN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 127, 127, 180, 185, 201, 201, 201, 201, 201, 72, 54, 43, 43, 13, 43, 13, 13, 1, 1, 1, 1, 13, 13, 54, 54, 180, 180, 201, 127, 72, 72, 43, 13, 1, 1, 1, 1, 1, 13, 54, 54, 54, 54] 201
rigid atoms, others: [34, 35, 36, 37, 38, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43])
total number of confs: 746
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051297 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(C3CC3)=NN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [49, 49, 49, 84, 91, 134, 134, 134, 134, 134, 19, 11, 7, 7, 1, 7, 1, 1, 1, 1, 13, 13, 1, 1, 11, 11, 84, 84, 134, 49, 19, 19, 7, 1, 13, 13, 13, 13, 13, 1, 11, 11, 11, 11] 201
rigid atoms, others: [33, 39, 14, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 450
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051297 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051297
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051297/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051297
Building REAL300025051298
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051298'
/scratch/stefan/7786831/working/building/REAL300025051298 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051298

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051298/0 /scratch/stefan/7786831/working/building/REAL300025051298 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 156)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/156
`/scratch/stefan/7786831/working/3D/156' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCC(F)(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051298.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051298.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051298/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051298 none O=C(CCCC(F)(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 15, 15, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [105, 105, 105, 176, 195, 201, 201, 201, 201, 105, 96, 50, 50, 26, 50, 13, 1, 1, 1, 1, 1, 1, 1, 105, 105, 176, 176, 201, 201, 201, 201, 105, 96, 96, 50, 26, 26, 1, 105, 105, 105, 105] 201
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41])
total number of confs: 939
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051298 none O=C(CCCC(F)(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 15, 15, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 9, 12, 14, 14, 14, 14, 1, 1, 1, 5, 8, 8, 8, 25, 36, 105, 105, 105, 105, 105, 1, 1, 9, 9, 14, 14, 14, 14, 2, 5, 5, 8, 25, 25, 105, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 284
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051298 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051298
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051298/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051298
Building REAL300025051299
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051299'
/scratch/stefan/7786831/working/building/REAL300025051299 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051299

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051299/0 /scratch/stefan/7786831/working/building/REAL300025051299 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 157)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/157
`/scratch/stefan/7786831/working/3D/157' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(F)=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051299.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051299.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051299/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051299 none CC1=CC(F)=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 19, 19, 19, 53, 65, 104, 104, 104, 104, 104, 1, 1, 5, 5, 5, 5, 5, 5, 2, 4, 4, 19, 53, 53, 104, 1, 1, 1, 1, 5] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42])
total number of confs: 292
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051299 none CC1=CC(F)=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 66, 66, 66, 134, 156, 201, 201, 201, 201, 201, 5, 5, 1, 2, 2, 2, 1, 1, 5, 13, 13, 66, 134, 134, 201, 5, 5, 5, 5, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 42, 25, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 637
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051299 none CC1=CC(F)=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 104, 104, 104, 104, 85, 57, 57, 25, 57, 13, 1, 1, 1, 1, 1, 1, 1, 104, 104, 201, 201, 201, 201, 201, 201, 104, 85, 85, 57, 25, 25, 1, 104, 104, 104, 104, 201] 201
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 529
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051299 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051299
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051299/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051299
Building REAL300025051300
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051300'
/scratch/stefan/7786831/working/building/REAL300025051300 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051300

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051300/0 /scratch/stefan/7786831/working/building/REAL300025051300 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 158)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/158
`/scratch/stefan/7786831/working/3D/158' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)CC(C)(C)C)

`REAL300025051300.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051300.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051300/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051300 none CC(CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)CC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 161, 161, 161, 161, 119, 50, 50, 29, 50, 13, 1, 1, 1, 1, 1, 1, 1, 161, 161, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 161, 119, 119, 50, 29, 29, 1, 161, 161, 161, 161, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [38, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 871
number of broken/clashed sets: 201
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051300 none CC(CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)CC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 2, 2, 1, 1, 1, 6, 17, 17, 17, 51, 63, 161, 161, 161, 161, 161, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 2, 6, 6, 17, 51, 51, 161, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 201
rigid atoms, others: [5, 6, 39, 40, 41, 42, 7, 19, 20] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 392
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051300 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051300
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051300/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051300
Building REAL300025051301
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051301'
/scratch/stefan/7786831/working/building/REAL300025051301 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051301

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051301/0 /scratch/stefan/7786831/working/building/REAL300025051301 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 159)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/159
`/scratch/stefan/7786831/working/3D/159' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1N=C(C)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051301.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051301.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051301/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051301 none CCN1N=C(C)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 5, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 6, 10, 10, 10, 36, 52, 167, 167, 167, 167, 167, 1, 1, 9, 9, 9, 9, 9, 5, 5, 5, 5, 2, 6, 6, 10, 36, 36, 167, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
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: REAL300025051301 none CCN1N=C(C)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 15, 22, 22, 22, 68, 89, 177, 177, 177, 177, 177, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 1, 5, 15, 15, 22, 68, 68, 177, 5, 5, 5, 5] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 34] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 475
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051301 none CCN1N=C(C)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 177, 177, 177, 177, 177, 177, 167, 167, 167, 167, 124, 65, 65, 27, 65, 13, 1, 1, 1, 1, 1, 1, 1, 167, 167, 201, 201, 201, 201, 201, 177, 177, 177, 177, 167, 124, 124, 65, 27, 27, 1, 167, 167, 167, 167] 201
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 822
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051301 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051301
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051301/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051301
Building REAL300025051302
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051302'
/scratch/stefan/7786831/working/building/REAL300025051302 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051302

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051302/0 /scratch/stefan/7786831/working/building/REAL300025051302 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 160)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/160
`/scratch/stefan/7786831/working/3D/160' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3=CC=CC=C3C2)CC1)

`REAL300025051302.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051302.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051302/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051302 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3=CC=CC=C3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 16, 16, 52, 64, 135, 135, 135, 135, 135, 5, 1, 1, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 52, 52, 135, 16, 5, 5, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 349
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051302 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3=CC=CC=C3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [66, 31, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 119, 135, 135, 135, 135, 201, 201, 201, 201, 201, 201, 201, 201, 135, 135, 31, 31, 1, 66, 119, 119, 135, 201, 201, 201, 201, 201, 201, 201, 201, 201, 135, 135, 135, 135] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46])
total number of confs: 737
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051302 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3=CC=CC=C3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [63, 63, 63, 141, 151, 201, 201, 201, 201, 201, 24, 17, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 141, 141, 201, 63, 24, 24, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46])
total number of confs: 677
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051302 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051302
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051302/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051302
Building REAL300025051303
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051303'
/scratch/stefan/7786831/working/building/REAL300025051303 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051303

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051303/0 /scratch/stefan/7786831/working/building/REAL300025051303 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 161)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/161
`/scratch/stefan/7786831/working/3D/161' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(Cl)C(F)=C2)CC1)

`REAL300025051303.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051303.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051303/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051303 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(Cl)C(F)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 15, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 60, 69, 108, 108, 108, 108, 108, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 1, 1, 60, 60, 108, 20, 5, 5, 3, 9, 9, 9, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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: REAL300025051303 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(Cl)C(F)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 15, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [54, 28, 13, 1, 1, 1, 1, 1, 1, 1, 54, 54, 87, 108, 108, 108, 108, 201, 201, 201, 201, 201, 201, 201, 108, 108, 28, 28, 1, 54, 87, 87, 108, 201, 201, 201, 108, 108, 108, 108] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 553
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051303 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(Cl)C(F)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 15, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 153, 169, 201, 201, 201, 201, 201, 17, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 153, 153, 201, 63, 17, 17, 5, 1, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [33, 34, 35, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39])
total number of confs: 695
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051303 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051303
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051303/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051303
Building REAL300025051304
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051304'
/scratch/stefan/7786831/working/building/REAL300025051304 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051304

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051304/0 /scratch/stefan/7786831/working/building/REAL300025051304 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 162)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/162
`/scratch/stefan/7786831/working/3D/162' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NOC3=C2CCCC3)CC1)

`REAL300025051304.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051304.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051304/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051304 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NOC3=C2CCCC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 29, 91, 95, 200, 200, 200, 200, 200, 6, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 91, 91, 200, 29, 6, 6, 3, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 515
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051304 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NOC3=C2CCCC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [52, 32, 13, 1, 1, 1, 1, 1, 1, 1, 52, 52, 131, 200, 200, 200, 200, 201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 32, 32, 1, 52, 131, 131, 200, 201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 200, 200] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45])
total number of confs: 748
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051304 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NOC3=C2CCCC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [50, 50, 50, 127, 130, 201, 201, 201, 201, 201, 11, 6, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 127, 127, 201, 50, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44, 45])
total number of confs: 628
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051304 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051304
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051304/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051304
Building REAL300025051305
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051305'
/scratch/stefan/7786831/working/building/REAL300025051305 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051305

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051305/0 /scratch/stefan/7786831/working/building/REAL300025051305 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 163)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/163
`/scratch/stefan/7786831/working/3D/163' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(F)=CC(Cl)=C2)CC1)

`REAL300025051305.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051305.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051305/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051305 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(F)=CC(Cl)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 15, 1, 1, 16, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 44, 51, 79, 79, 79, 79, 79, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 1, 1, 44, 44, 79, 18, 5, 5, 3, 9, 9, 9, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
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: REAL300025051305 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(F)=CC(Cl)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 15, 1, 1, 16, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [42, 26, 13, 1, 1, 1, 1, 1, 1, 1, 42, 42, 71, 79, 79, 79, 79, 201, 201, 201, 201, 201, 201, 201, 79, 79, 26, 26, 1, 42, 71, 71, 79, 201, 201, 201, 79, 79, 79, 79] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 484
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051305 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(F)=CC(Cl)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 15, 1, 1, 16, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 139, 157, 201, 201, 201, 201, 201, 17, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 139, 139, 201, 65, 17, 17, 5, 1, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [33, 34, 35, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39])
total number of confs: 664
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051305 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051305
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051305/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051305
Building REAL300025051306
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051306'
/scratch/stefan/7786831/working/building/REAL300025051306 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051306

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051306/0 /scratch/stefan/7786831/working/building/REAL300025051306 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 164)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/164
`/scratch/stefan/7786831/working/3D/164' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(F)=CC=C2Cl)CC1)

`REAL300025051306.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051306.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051306/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051306 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(F)=CC=C2Cl)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 15, 1, 1, 1, 16, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 72, 89, 162, 162, 162, 162, 162, 5, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 1, 1, 72, 72, 162, 22, 5, 5, 3, 13, 13, 13, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
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: REAL300025051306 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(F)=CC=C2Cl)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 15, 1, 1, 1, 16, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [71, 32, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 129, 162, 162, 162, 162, 201, 201, 201, 201, 201, 201, 201, 162, 162, 32, 32, 1, 71, 129, 129, 162, 201, 201, 201, 162, 162, 162, 162] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 675
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051306 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(F)=CC=C2Cl)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 15, 1, 1, 1, 16, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 144, 160, 201, 201, 201, 201, 201, 20, 13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 144, 144, 201, 64, 20, 20, 7, 1, 1, 1, 13, 13, 13, 13] 201
rigid atoms, others: [33, 34, 35, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39])
total number of confs: 663
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051306 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051306
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051306/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051306
Building REAL300025051307
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051307'
/scratch/stefan/7786831/working/building/REAL300025051307 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051307

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051307/0 /scratch/stefan/7786831/working/building/REAL300025051307 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 165)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/165
`/scratch/stefan/7786831/working/3D/165' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=NC=C2Cl)CC1)

`REAL300025051307.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051307.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051307/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051307 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=NC=C2Cl)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 16, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 23, 23, 76, 92, 170, 170, 170, 170, 170, 5, 1, 1, 1, 3, 3, 3, 13, 13, 5, 13, 13, 13, 1, 1, 76, 76, 170, 23, 5, 5, 3, 13, 13, 13, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 469
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051307 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=NC=C2Cl)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 16, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [72, 33, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 136, 170, 170, 170, 170, 201, 201, 201, 201, 201, 201, 170, 170, 33, 33, 1, 72, 136, 136, 170, 201, 201, 201, 170, 170, 170, 170] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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])
total number of confs: 710
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051307 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=NC=C2Cl)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 16, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [65, 65, 65, 137, 151, 201, 201, 201, 201, 201, 20, 13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 13, 13, 137, 137, 201, 65, 20, 20, 7, 1, 1, 1, 13, 13, 13, 13] 201
rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38])
total number of confs: 643
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051307 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051307
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051307/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051307
Building REAL300025051308
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051308'
/scratch/stefan/7786831/working/building/REAL300025051308 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051308

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051308/0 /scratch/stefan/7786831/working/building/REAL300025051308 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 166)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/166
`/scratch/stefan/7786831/working/3D/166' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(F)=C1)

`REAL300025051308.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051308.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051308/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051308 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 2, 6, 6, 2, 2, 2, 1, 1, 1, 7, 26, 26, 26, 80, 93, 186, 187, 187, 187, 187, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 7, 7, 26, 80, 80, 187, 1, 1, 1, 1, 6] 201
rigid atoms, others: [38, 7, 8, 9, 39, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 42])
total number of confs: 499
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051308 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 6, 6, 20, 57, 57, 57, 130, 140, 200, 201, 201, 201, 201, 6, 6, 1, 1, 1, 2, 2, 2, 1, 1, 6, 20, 20, 57, 130, 130, 201, 6, 6, 6, 6, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 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])
total number of confs: 635
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051308 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 187, 201, 201, 187, 187, 187, 187, 118, 50, 50, 28, 50, 13, 1, 1, 1, 1, 1, 1, 1, 187, 187, 201, 201, 201, 201, 201, 201, 201, 201, 187, 118, 118, 50, 28, 28, 1, 187, 187, 187, 187, 201] 201
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 791
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051308 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051308
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051308/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051308
Building REAL300025051309
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051309'
/scratch/stefan/7786831/working/building/REAL300025051309 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051309

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051309/0 /scratch/stefan/7786831/working/building/REAL300025051309 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 167)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/167
`/scratch/stefan/7786831/working/3D/167' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC=C1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051309.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051309.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051309/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051309 none CC1=CC=CC=C1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 20, 20, 20, 20, 12, 10, 2, 2, 2, 1, 1, 1, 5, 7, 7, 7, 26, 39, 106, 106, 106, 106, 106, 1, 1, 20, 20, 20, 20, 20, 20, 20, 12, 12, 10, 10, 2, 5, 5, 7, 26, 26, 106, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 46, 45, 48, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
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: REAL300025051309 none CC1=CC=CC=C1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 20, 20, 20, 20, 44, 58, 58, 58, 96, 125, 201, 201, 201, 201, 201, 20, 20, 2, 2, 2, 1, 1, 1, 1, 3, 3, 5, 5, 20, 44, 44, 58, 96, 96, 201, 20, 20, 20, 20] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 33, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 631
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051309 none CC1=CC=CC=C1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 173, 171, 106, 106, 106, 106, 90, 52, 52, 27, 52, 12, 1, 1, 1, 1, 1, 1, 1, 106, 106, 201, 201, 201, 201, 201, 201, 201, 173, 173, 171, 171, 106, 90, 90, 52, 27, 27, 1, 106, 106, 106, 106] 201
rigid atoms, others: [44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48])
total number of confs: 810
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051309 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051309
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051309/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051309
Building REAL300025051310
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051310'
/scratch/stefan/7786831/working/building/REAL300025051310 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051310

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051310/0 /scratch/stefan/7786831/working/building/REAL300025051310 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 168)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/168
`/scratch/stefan/7786831/working/3D/168' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2C3CCCCCCC32)CC1)

`REAL300025051310.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051310.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051310/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051310 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2C3CCCCCCC32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 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: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 29, 99, 108, 183, 183, 183, 183, 183, 6, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 99, 99, 183, 29, 6, 6, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 49, 50, 51, 52, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 520
number of broken/clashed sets: 201
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051310 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2C3CCCCCCC32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 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: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 31, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 147, 183, 183, 183, 183, 201, 201, 201, 201, 201, 201, 201, 201, 183, 183, 31, 31, 1, 72, 147, 147, 183, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 183, 183, 183, 183] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 764
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051310 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2C3CCCCCCC32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 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: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 129, 140, 201, 201, 201, 201, 201, 16, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 129, 129, 201, 52, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 49, 50, 51, 52])
total number of confs: 620
number of broken/clashed sets: 201
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051310 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051310
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051310/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051310
Building REAL300025051311
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051311'
/scratch/stefan/7786831/working/building/REAL300025051311 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051311

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051311/0 /scratch/stefan/7786831/working/building/REAL300025051311 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 169)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/169
`/scratch/stefan/7786831/working/3D/169' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC23CC3)CC1)

`REAL300025051311.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051311.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051311/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051311 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC23CC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 16, 16, 57, 64, 139, 139, 139, 139, 139, 5, 1, 1, 1, 3, 3, 3, 18, 18, 18, 18, 1, 1, 57, 57, 139, 16, 5, 5, 3, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
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: REAL300025051311 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC23CC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [74, 33, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 125, 139, 139, 139, 139, 201, 201, 201, 201, 139, 139, 33, 33, 1, 74, 125, 125, 139, 201, 201, 201, 201, 201, 201, 201, 139, 139, 139, 139] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 25] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 737
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051311 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC23CC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [70, 70, 70, 142, 150, 201, 201, 201, 201, 201, 24, 18, 11, 11, 1, 11, 1, 1, 1, 1, 1, 18, 18, 142, 142, 201, 70, 24, 24, 11, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18] 201
rigid atoms, others: [32, 33, 34, 35, 36, 14, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40])
total number of confs: 672
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051311 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051311
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051311/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051311
Building REAL300025051312
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051312'
/scratch/stefan/7786831/working/building/REAL300025051312 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051312

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051312/0 /scratch/stefan/7786831/working/building/REAL300025051312 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 170)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/170
`/scratch/stefan/7786831/working/3D/170' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC3=CC=NC=C3C=C2)CC1)

`REAL300025051312.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051312.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051312/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051312 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC3=CC=NC=C3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [31, 31, 31, 99, 110, 198, 198, 198, 198, 198, 7, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 99, 99, 198, 31, 7, 7, 3, 7, 7, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 534
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051312 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC3=CC=NC=C3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [65, 31, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 146, 198, 198, 198, 198, 201, 201, 201, 201, 201, 201, 201, 201, 201, 198, 198, 31, 31, 1, 65, 146, 146, 198, 201, 201, 201, 201, 201, 198, 198, 198, 198] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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])
total number of confs: 738
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051312 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC3=CC=NC=C3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [49, 49, 49, 132, 138, 201, 201, 201, 201, 201, 12, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 132, 132, 201, 49, 12, 12, 4, 1, 1, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43])
total number of confs: 617
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051312 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051312
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051312/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051312
Building REAL300025051313
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051313'
/scratch/stefan/7786831/working/building/REAL300025051313 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051313

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051313/0 /scratch/stefan/7786831/working/building/REAL300025051313 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 171)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/171
`/scratch/stefan/7786831/working/3D/171' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC(F)=C2Cl)CC1)

`REAL300025051313.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051313.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051313/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051313 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC(F)=C2Cl)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 16, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 76, 95, 179, 179, 179, 179, 179, 5, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 1, 1, 76, 76, 179, 23, 5, 5, 3, 11, 11, 11, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 460
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051313 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC(F)=C2Cl)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 16, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [82, 34, 13, 1, 1, 1, 1, 1, 1, 1, 82, 82, 147, 179, 179, 179, 179, 201, 201, 201, 201, 201, 201, 201, 179, 179, 34, 34, 1, 82, 147, 147, 179, 201, 201, 201, 179, 179, 179, 179] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 712
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051313 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC(F)=C2Cl)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 16, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 138, 155, 201, 201, 201, 201, 201, 18, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 138, 138, 201, 62, 18, 18, 7, 1, 1, 1, 11, 11, 11, 11] 201
rigid atoms, others: [33, 34, 35, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39])
total number of confs: 648
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051313 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051313
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051313/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051313
Building REAL300025051314
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051314'
/scratch/stefan/7786831/working/building/REAL300025051314 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051314

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051314/0 /scratch/stefan/7786831/working/building/REAL300025051314 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 172)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/172
`/scratch/stefan/7786831/working/3D/172' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC(F)(F)CC2)CC1)

`REAL300025051314.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051314.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051314/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051314 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC(F)(F)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 60, 73, 148, 148, 148, 148, 148, 5, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 1, 1, 60, 60, 148, 18, 5, 5, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
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: REAL300025051314 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC(F)(F)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [71, 33, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 121, 148, 148, 148, 148, 201, 201, 201, 201, 201, 201, 201, 148, 148, 33, 33, 1, 71, 121, 121, 148, 201, 201, 201, 201, 201, 201, 201, 201, 201, 148, 148, 148, 148] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 740
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051314 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC(F)(F)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 140, 151, 201, 201, 201, 201, 201, 19, 14, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 140, 140, 201, 65, 19, 19, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45])
total number of confs: 675
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051314 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051314
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051314/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051314
Building REAL300025051315
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051315'
/scratch/stefan/7786831/working/building/REAL300025051315 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051315

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051315/0 /scratch/stefan/7786831/working/building/REAL300025051315 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 173)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/173
`/scratch/stefan/7786831/working/3D/173' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=NC3=CC=CC=C32)CC1)

`REAL300025051315.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051315.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051315/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051315 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=NC3=CC=CC=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'N.ar', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [19, 19, 19, 49, 58, 126, 126, 126, 126, 126, 5, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 49, 49, 126, 19, 5, 5, 3, 13, 13, 13, 13, 13, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 315
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051315 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=NC3=CC=CC=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'N.ar', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [52, 28, 13, 1, 1, 1, 1, 1, 1, 1, 52, 52, 93, 126, 126, 126, 126, 201, 201, 201, 201, 201, 201, 201, 201, 201, 126, 126, 28, 28, 1, 52, 93, 93, 126, 201, 201, 201, 201, 201, 126, 126, 126, 126] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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])
total number of confs: 590
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051315 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=NC3=CC=CC=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'N.ar', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [67, 67, 67, 121, 136, 201, 201, 201, 201, 201, 21, 13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 121, 121, 201, 67, 21, 21, 7, 1, 1, 1, 1, 1, 13, 13, 13, 13] 201
rigid atoms, others: [35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43])
total number of confs: 621
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051315 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051315
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051315/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051315
Building REAL300025051316
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051316'
/scratch/stefan/7786831/working/building/REAL300025051316 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051316

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051316/0 /scratch/stefan/7786831/working/building/REAL300025051316 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 174)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/174
`/scratch/stefan/7786831/working/3D/174' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(F)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051316.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051316.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051316/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051316 none CC1=CC=C(F)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 2, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 27, 27, 27, 77, 90, 189, 190, 190, 190, 190, 1, 1, 4, 4, 4, 4, 4, 4, 2, 7, 7, 27, 77, 77, 190, 1, 1, 1, 1, 4] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42])
total number of confs: 482
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051316 none CC1=CC=C(F)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 17, 56, 56, 56, 133, 146, 200, 201, 201, 201, 201, 4, 4, 1, 2, 2, 2, 1, 1, 4, 17, 17, 56, 133, 133, 201, 4, 4, 4, 4, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 42, 25, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 642
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051316 none CC1=CC=C(F)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 190, 201, 201, 201, 190, 190, 190, 190, 121, 49, 49, 27, 49, 13, 1, 1, 1, 1, 1, 1, 1, 190, 190, 201, 201, 201, 201, 201, 201, 190, 121, 121, 49, 27, 27, 1, 190, 190, 190, 190, 201] 201
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 762
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051316 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051316
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051316/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051316
Building REAL300025051317
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051317'
/scratch/stefan/7786831/working/building/REAL300025051317 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051317

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051317/0 /scratch/stefan/7786831/working/building/REAL300025051317 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 175)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/175
`/scratch/stefan/7786831/working/3D/175' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(NS(C)(=O)=O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051317.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051317.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051317/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051317 none CC(NS(C)(=O)=O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 14, 5, 11, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 7, 6, 6, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [199, 154, 199, 201, 201, 201, 201, 154, 154, 154, 125, 61, 61, 28, 61, 13, 1, 1, 1, 1, 1, 1, 1, 154, 154, 199, 199, 199, 199, 201, 201, 201, 201, 154, 125, 125, 61, 28, 28, 1, 154, 154, 154, 154] 201
rigid atoms, others: [39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 844
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051317 none CC(NS(C)(=O)=O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 14, 5, 11, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 7, 6, 6, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 2, 7, 11, 18, 18, 18, 2, 2, 1, 1, 1, 7, 20, 20, 20, 44, 62, 154, 154, 154, 154, 154, 1, 1, 7, 7, 7, 7, 11, 18, 18, 18, 2, 7, 7, 20, 44, 44, 154, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 406
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051317 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051317
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051317/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051317
Building REAL300025051318
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051318'
/scratch/stefan/7786831/working/building/REAL300025051318 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051318

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051318/0 /scratch/stefan/7786831/working/building/REAL300025051318 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 176)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/176
`/scratch/stefan/7786831/working/3D/176' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(=O)N1)

`REAL300025051318.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051318.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051318/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051318 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 28, 28, 28, 90, 110, 197, 198, 198, 198, 198, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 28, 90, 90, 198, 1, 1, 1, 1, 4] 201
rigid atoms, others: [38, 7, 8, 9, 39, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 42])
total number of confs: 533
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051318 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 14, 41, 41, 41, 108, 126, 200, 201, 201, 201, 201, 4, 4, 1, 1, 1, 2, 2, 2, 1, 1, 4, 14, 14, 41, 108, 108, 201, 4, 4, 4, 4, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 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])
total number of confs: 589
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051318 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 198, 198, 198, 198, 135, 66, 66, 31, 66, 13, 1, 1, 1, 1, 1, 1, 1, 198, 198, 201, 201, 201, 201, 201, 201, 201, 201, 198, 135, 135, 66, 31, 31, 1, 198, 198, 198, 198, 201] 201
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 725
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051318 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051318
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051318/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051318
Building REAL300025051319
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051319'
/scratch/stefan/7786831/working/building/REAL300025051319 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051319

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051319/0 /scratch/stefan/7786831/working/building/REAL300025051319 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 177)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/177
`/scratch/stefan/7786831/working/3D/177' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=CC=CC=C3N=C2)CC1)

`REAL300025051319.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051319.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051319/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051319 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=CC=CC=C3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 72, 88, 133, 133, 133, 133, 133, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 72, 72, 133, 22, 5, 5, 3, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 42, 11, 12, 13, 44, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 382
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051319 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=CC=CC=C3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 107, 133, 133, 133, 133, 201, 201, 201, 201, 201, 201, 201, 201, 201, 133, 133, 32, 32, 1, 70, 107, 107, 133, 201, 201, 201, 201, 201, 201, 133, 133, 133, 133] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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])
total number of confs: 607
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051319 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=CC=CC=C3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 152, 171, 201, 201, 201, 201, 201, 16, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 152, 152, 201, 64, 16, 16, 5, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [35, 36, 37, 38, 39, 40, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44])
total number of confs: 677
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051319 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051319
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051319/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051319
Building REAL300025051320
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051320'
/scratch/stefan/7786831/working/building/REAL300025051320 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051320

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051320/0 /scratch/stefan/7786831/working/building/REAL300025051320 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 178)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/178
`/scratch/stefan/7786831/working/3D/178' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3C=CNC3=C2)CC1)

`REAL300025051320.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051320.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051320/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051320 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3C=CNC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 19, 62, 74, 117, 117, 117, 117, 117, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 62, 62, 117, 19, 5, 5, 3, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
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: REAL300025051320 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3C=CNC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [70, 31, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 102, 117, 117, 117, 117, 201, 201, 201, 201, 201, 201, 201, 201, 117, 117, 31, 31, 1, 70, 102, 102, 117, 201, 201, 201, 201, 201, 201, 117, 117, 117, 117] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 574
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051320 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3C=CNC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 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]
0  hydrogens 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, 157, 171, 201, 201, 201, 201, 201, 17, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 157, 157, 201, 64, 17, 17, 5, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43])
total number of confs: 694
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051320 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051320
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051320/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051320
Building REAL300025051321
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051321'
/scratch/stefan/7786831/working/building/REAL300025051321 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051321

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051321/0 /scratch/stefan/7786831/working/building/REAL300025051321 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 179)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/179
`/scratch/stefan/7786831/working/3D/179' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051321.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051321.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051321/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051321 none CCOC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
147  conformations in input
total number of sets (complete confs): 147
using faster count positions algorithm for large data
unique positions, atoms: [22, 20, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 3, 5, 5, 5, 8, 17, 76, 76, 76, 76, 76, 1, 1, 5, 22, 22, 22, 22, 22, 5, 5, 5, 2, 3, 3, 5, 8, 8, 76, 1, 1, 1, 1, 5] 147
rigid atoms, others: [43, 44, 10, 11, 12, 45, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46])
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: REAL300025051321 none CCOC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
147  conformations in input
total number of sets (complete confs): 147
using faster count positions algorithm for large data
unique positions, atoms: [9, 7, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 10, 10, 10, 16, 35, 124, 124, 124, 124, 124, 5, 5, 1, 9, 9, 9, 9, 9, 1, 1, 1, 5, 8, 8, 10, 16, 16, 124, 5, 5, 5, 5, 1] 147
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 46, 26] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 236
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051321 none CCOC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
147  conformations in input
total number of sets (complete confs): 147
using faster count positions algorithm for large data
unique positions, atoms: [147, 147, 124, 124, 124, 124, 124, 76, 76, 76, 76, 61, 54, 54, 36, 54, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 124, 147, 147, 147, 147, 147, 124, 124, 124, 76, 61, 61, 54, 36, 36, 1, 76, 76, 76, 76, 124] 147
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46])
total number of confs: 414
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051321 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051321
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051321/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051321
Building REAL300025051322
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051322'
/scratch/stefan/7786831/working/building/REAL300025051322 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051322

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051322/0 /scratch/stefan/7786831/working/building/REAL300025051322 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 180)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/180
`/scratch/stefan/7786831/working/3D/180' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1C)

`REAL300025051322.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051322.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051322/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051322 none COC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 7, 7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 6, 10, 10, 10, 33, 50, 157, 157, 157, 157, 157, 1, 1, 7, 7, 16, 16, 16, 7, 7, 7, 2, 6, 6, 10, 33, 33, 157, 1, 1, 1, 1, 7, 7, 7] 201
rigid atoms, others: [43, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46])
total number of confs: 328
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051322 none COC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 19, 28, 28, 28, 69, 96, 201, 201, 201, 201, 201, 7, 7, 1, 1, 4, 4, 4, 1, 1, 1, 7, 19, 19, 28, 69, 69, 201, 7, 7, 7, 7, 2, 2, 2] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 25, 26, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 509
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051322 none COC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 157, 157, 157, 157, 114, 65, 65, 29, 65, 13, 1, 1, 1, 1, 1, 1, 1, 157, 157, 201, 201, 201, 201, 201, 201, 201, 201, 157, 114, 114, 65, 29, 29, 1, 157, 157, 157, 157, 201, 201, 201] 201
rigid atoms, others: [39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 705
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051322 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051322
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051322/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051322
Building REAL300025051323
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051323'
/scratch/stefan/7786831/working/building/REAL300025051323 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051323

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051323/0 /scratch/stefan/7786831/working/building/REAL300025051323 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 181)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/181
`/scratch/stefan/7786831/working/3D/181' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CNC=N2)CC1)

`REAL300025051323.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051323.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051323/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051323 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CNC=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
129  conformations in input
total number of sets (complete confs): 129
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 21, 27, 61, 61, 61, 61, 61, 4, 1, 1, 1, 3, 3, 3, 24, 51, 51, 51, 51, 1, 1, 21, 21, 61, 11, 4, 4, 3, 24, 24, 51, 51, 51, 1, 1, 1, 1] 129
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 255
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051323 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CNC=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
129  conformations in input
total number of sets (complete confs): 129
using faster count positions algorithm for large data
unique positions, atoms: [35, 23, 13, 1, 1, 1, 1, 1, 1, 1, 35, 35, 56, 61, 61, 61, 61, 124, 129, 129, 129, 129, 61, 61, 23, 23, 1, 35, 56, 56, 61, 124, 124, 129, 129, 129, 61, 61, 61, 61] 129
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 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: 527
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051323 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CNC=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
129  conformations in input
total number of sets (complete confs): 129
using faster count positions algorithm for large data
unique positions, atoms: [100, 100, 100, 112, 115, 129, 129, 129, 129, 129, 61, 51, 40, 40, 9, 40, 1, 1, 1, 1, 1, 1, 51, 51, 112, 112, 129, 100, 61, 61, 40, 9, 9, 1, 1, 1, 51, 51, 51, 51] 129
rigid atoms, others: [33, 34, 35, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39])
total number of confs: 437
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051323 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051323/1 /scratch/stefan/7786831/working/building/REAL300025051323 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 182)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/182
`/scratch/stefan/7786831/working/3D/182' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CN=CN2)CC1)

`REAL300025051323.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051323.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051323/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051323 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CN=CN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [19, 19, 19, 56, 69, 147, 147, 147, 147, 147, 6, 1, 1, 1, 3, 3, 3, 20, 32, 32, 32, 32, 1, 1, 56, 56, 147, 19, 6, 6, 3, 20, 20, 32, 32, 32, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
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: REAL300025051323 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CN=CN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [76, 30, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 124, 147, 147, 147, 147, 188, 201, 201, 201, 201, 147, 147, 30, 30, 1, 76, 124, 124, 147, 188, 188, 201, 201, 201, 147, 147, 147, 147] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 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: 774
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051323 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CN=CN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [80, 80, 80, 137, 152, 201, 201, 201, 201, 201, 42, 32, 25, 25, 4, 25, 1, 1, 1, 1, 1, 1, 32, 32, 137, 137, 201, 80, 42, 42, 25, 4, 4, 1, 1, 1, 32, 32, 32, 32] 201
rigid atoms, others: [33, 34, 35, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39])
total number of confs: 659
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051323 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051323
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051323/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051323/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051323
Building REAL300025051324
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051324'
/scratch/stefan/7786831/working/building/REAL300025051324 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051324

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051324/0 /scratch/stefan/7786831/working/building/REAL300025051324 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 183)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/183
`/scratch/stefan/7786831/working/3D/183' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CC=CC(F)=C2F)CC1)

`REAL300025051324.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051324.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051324/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051324 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CC=CC(F)=C2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 15, 1, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 17, 50, 60, 134, 134, 134, 134, 134, 5, 1, 1, 1, 3, 3, 3, 17, 27, 27, 27, 27, 27, 27, 27, 1, 1, 50, 50, 134, 17, 5, 5, 3, 17, 17, 27, 27, 27, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
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: REAL300025051324 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CC=CC(F)=C2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 15, 1, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [58, 29, 13, 1, 1, 1, 1, 1, 1, 1, 58, 58, 109, 134, 134, 134, 134, 194, 201, 201, 201, 201, 201, 201, 201, 134, 134, 29, 29, 1, 58, 109, 109, 134, 194, 194, 201, 201, 201, 134, 134, 134, 134] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 812
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051324 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CC=CC(F)=C2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 15, 1, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [68, 68, 68, 128, 137, 201, 201, 201, 201, 201, 36, 27, 21, 21, 6, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 128, 128, 201, 68, 36, 36, 21, 6, 6, 1, 1, 1, 27, 27, 27, 27] 201
rigid atoms, others: [36, 37, 38, 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, 39, 40, 41, 42])
total number of confs: 659
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051324 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051324
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051324/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051324
Building REAL300025051325
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051325'
/scratch/stefan/7786831/working/building/REAL300025051325 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051325

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051325/0 /scratch/stefan/7786831/working/building/REAL300025051325 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 184)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/184
`/scratch/stefan/7786831/working/3D/184' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCCCCC2)CC1)

`REAL300025051325.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051325.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051325/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051325 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCCCCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 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: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 15, 31, 34, 70, 70, 70, 70, 70, 5, 1, 1, 1, 3, 3, 3, 19, 46, 46, 46, 46, 46, 46, 1, 1, 31, 31, 70, 15, 5, 5, 3, 19, 19, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 48, 49, 50, 51, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025051325 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCCCCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 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: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [33, 22, 13, 1, 1, 1, 1, 1, 1, 1, 33, 33, 60, 70, 70, 70, 70, 174, 201, 201, 201, 201, 201, 201, 70, 70, 22, 22, 1, 33, 60, 60, 70, 174, 174, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 70, 70, 70, 70] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 773
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051325 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCCCCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 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: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 127, 127, 186, 190, 201, 201, 201, 201, 201, 59, 46, 28, 28, 7, 28, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 186, 186, 201, 127, 59, 59, 28, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46] 201
rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 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, 48, 49, 50, 51])
total number of confs: 780
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051325 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051325
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051325/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051325
Building REAL300025051326
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051326'
/scratch/stefan/7786831/working/building/REAL300025051326 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051326

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051326/0 /scratch/stefan/7786831/working/building/REAL300025051326 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 185)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/185
`/scratch/stefan/7786831/working/3D/185' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)N1)

`REAL300025051326.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051326.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051326/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051326 none CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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: [4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 25, 25, 25, 81, 95, 182, 182, 182, 182, 182, 1, 1, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 25, 81, 81, 182, 1, 1, 1, 1, 4, 4, 4, 4] 201
rigid atoms, others: [36, 37, 6, 7, 8, 39, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 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, 40, 41, 42, 43])
total number of confs: 484
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051326 none CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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: [1, 1, 1, 1, 1, 3, 3, 4, 4, 16, 53, 53, 53, 123, 138, 201, 201, 201, 201, 201, 4, 4, 1, 1, 1, 2, 2, 2, 1, 4, 16, 16, 53, 123, 123, 201, 4, 4, 4, 4, 2, 2, 2, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 43, 22, 23, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 629
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051326 none CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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, 182, 182, 182, 182, 126, 55, 55, 26, 55, 12, 1, 1, 1, 1, 1, 1, 1, 182, 182, 201, 201, 201, 201, 201, 201, 201, 182, 126, 126, 55, 26, 26, 1, 182, 182, 182, 182, 201, 201, 201, 201] 201
rigid atoms, others: [35, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 709
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051326 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051326
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051326/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051326
Building REAL300025051327
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051327'
/scratch/stefan/7786831/working/building/REAL300025051327 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051327

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051327/0 /scratch/stefan/7786831/working/building/REAL300025051327 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 186)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/186
`/scratch/stefan/7786831/working/3D/186' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C(F)C2=CC=CC=C2)CC1)

`REAL300025051327.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051327.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051327/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051327 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C(F)C2=CC=CC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 15, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 75, 88, 146, 146, 146, 146, 146, 6, 1, 1, 1, 3, 3, 3, 14, 14, 16, 16, 14, 16, 16, 1, 1, 75, 75, 146, 22, 6, 6, 3, 14, 16, 16, 16, 16, 16, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 450
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051327 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C(F)C2=CC=CC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 15, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [66, 26, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 124, 146, 146, 146, 146, 201, 201, 201, 201, 201, 201, 201, 146, 146, 26, 26, 1, 66, 124, 124, 146, 201, 201, 201, 201, 201, 201, 146, 146, 146, 146] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 838
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051327 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C(F)C2=CC=CC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 15, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [65, 65, 65, 153, 164, 201, 201, 201, 201, 201, 25, 16, 11, 11, 3, 11, 1, 3, 1, 1, 1, 1, 1, 1, 16, 16, 153, 153, 201, 65, 25, 25, 11, 3, 1, 1, 1, 1, 1, 16, 16, 16, 16] 201
rigid atoms, others: [34, 35, 36, 37, 38, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42])
total number of confs: 689
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051327 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051327
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051327/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051327
Building REAL300025051328
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051328'
/scratch/stefan/7786831/working/building/REAL300025051328 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051328

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051328/0 /scratch/stefan/7786831/working/building/REAL300025051328 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 187)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/187
`/scratch/stefan/7786831/working/3D/187' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC23CCC3)CC1)

`REAL300025051328.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051328.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051328/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051328 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC23CCC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 18, 59, 72, 149, 149, 149, 149, 149, 5, 1, 1, 1, 3, 3, 3, 18, 18, 18, 18, 18, 1, 1, 59, 59, 149, 18, 5, 5, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 390
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051328 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC23CCC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [70, 31, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 129, 149, 149, 149, 149, 201, 201, 201, 201, 201, 149, 149, 31, 31, 1, 70, 129, 129, 149, 201, 201, 201, 201, 201, 201, 201, 201, 201, 149, 149, 149, 149] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 749
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051328 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC23CCC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [68, 68, 68, 140, 154, 201, 201, 201, 201, 201, 25, 18, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 18, 18, 140, 140, 201, 68, 25, 25, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43])
total number of confs: 660
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051328 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051328
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051328/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051328
Building REAL300025051329
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051329'
/scratch/stefan/7786831/working/building/REAL300025051329 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051329

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051329/0 /scratch/stefan/7786831/working/building/REAL300025051329 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 188)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/188
`/scratch/stefan/7786831/working/3D/188' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2CC(=O)NC(=O)N2)CC1)

`REAL300025051329.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051329.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051329/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051329 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2CC(=O)NC(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 15, 38, 38, 78, 78, 78, 78, 78, 4, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 38, 38, 78, 15, 4, 4, 3, 14, 14, 14, 14, 1, 1, 1, 1] 91
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
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: REAL300025051329 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2CC(=O)NC(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [48, 30, 12, 1, 1, 1, 1, 1, 1, 1, 48, 48, 70, 78, 78, 78, 78, 91, 91, 91, 91, 91, 91, 91, 91, 78, 78, 30, 30, 1, 48, 70, 70, 78, 91, 91, 91, 91, 78, 78, 78, 78] 91
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 349
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051329 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2CC(=O)NC(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [38, 38, 38, 72, 72, 91, 91, 91, 91, 91, 19, 14, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 72, 72, 91, 38, 19, 19, 9, 1, 1, 1, 1, 14, 14, 14, 14] 91
rigid atoms, others: [34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 301
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051329 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051329
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051329/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051329
Building REAL300025051330
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051330'
/scratch/stefan/7786831/working/building/REAL300025051330 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051330

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051330/0 /scratch/stefan/7786831/working/building/REAL300025051330 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 189)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/189
`/scratch/stefan/7786831/working/3D/189' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC(C(C)C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051330.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051330.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051330/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051330 none CC1=CC=CC(C(C)C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 7, 7, 4, 2, 4, 2, 2, 1, 1, 1, 6, 16, 16, 16, 48, 59, 132, 132, 132, 132, 132, 1, 1, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 2, 6, 6, 16, 48, 48, 132, 1, 1, 1, 1, 7] 201
rigid atoms, others: [44, 10, 11, 12, 45, 46, 47, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48])
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: REAL300025051330 none CC1=CC=CC(C(C)C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 18, 39, 39, 39, 97, 117, 201, 201, 201, 201, 201, 7, 7, 1, 2, 2, 2, 1, 1, 1, 3, 3, 3, 3, 7, 18, 18, 39, 97, 97, 201, 7, 7, 7, 7, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 48, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 579
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051330 none CC1=CC=CC(C(C)C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 144, 132, 144, 132, 132, 132, 95, 48, 48, 25, 48, 13, 1, 1, 1, 1, 1, 1, 1, 132, 132, 201, 201, 201, 201, 201, 201, 201, 144, 144, 144, 144, 132, 95, 95, 48, 25, 25, 1, 132, 132, 132, 132, 201] 201
rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48])
total number of confs: 696
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051330 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051330
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051330/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051330
Building REAL300025051331
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051331'
/scratch/stefan/7786831/working/building/REAL300025051331 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051331

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051331/0 /scratch/stefan/7786831/working/building/REAL300025051331 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 190)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/190
`/scratch/stefan/7786831/working/3D/190' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C=C(Cl)C=N2)CC1)

`REAL300025051331.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051331.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051331/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051331 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C=C(Cl)C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 1, 1, 16, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 25, 28, 68, 68, 68, 68, 68, 4, 1, 1, 1, 3, 3, 3, 23, 62, 62, 62, 62, 62, 1, 1, 25, 25, 68, 11, 4, 4, 3, 23, 23, 62, 62, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 285
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051331 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C=C(Cl)C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 1, 1, 16, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [46, 25, 13, 1, 1, 1, 1, 1, 1, 1, 46, 46, 64, 68, 68, 68, 68, 151, 201, 201, 201, 201, 201, 68, 68, 25, 25, 1, 46, 64, 64, 68, 151, 151, 201, 201, 68, 68, 68, 68] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 702
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051331 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C=C(Cl)C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 1, 1, 16, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [140, 140, 140, 168, 176, 201, 201, 201, 201, 201, 74, 62, 49, 49, 9, 49, 1, 1, 1, 1, 1, 1, 1, 62, 62, 168, 168, 201, 140, 74, 74, 49, 9, 9, 1, 1, 62, 62, 62, 62] 201
rigid atoms, others: [34, 35, 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, 36, 37, 38, 39])
total number of confs: 661
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051331 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051331
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051331/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051331
Building REAL300025051332
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051332'
/scratch/stefan/7786831/working/building/REAL300025051332 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051332

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051332/0 /scratch/stefan/7786831/working/building/REAL300025051332 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 191)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/191
`/scratch/stefan/7786831/working/3D/191' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1)

`REAL300025051332.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051332.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051332/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051332 none CCC1=CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 5, 5, 10, 10, 5, 2, 2, 2, 1, 1, 1, 5, 13, 13, 13, 46, 69, 133, 133, 133, 133, 133, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 2, 5, 5, 13, 46, 46, 133, 1, 1, 1, 1, 10, 10] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 46, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48])
total number of confs: 379
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051332 none CCC1=CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 10, 10, 10, 10, 23, 39, 39, 39, 93, 124, 201, 201, 201, 201, 201, 10, 10, 1, 1, 2, 2, 2, 1, 1, 1, 1, 5, 5, 10, 23, 23, 39, 93, 93, 201, 10, 10, 10, 10, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 47, 33, 48, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 597
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051332 none CCC1=CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 142, 142, 201, 201, 142, 133, 133, 133, 133, 112, 67, 67, 31, 67, 13, 1, 1, 1, 1, 1, 1, 1, 133, 133, 201, 201, 201, 201, 201, 201, 201, 201, 201, 142, 142, 133, 112, 112, 67, 31, 31, 1, 133, 133, 133, 133, 201, 201] 201
rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48])
total number of confs: 1170
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051332 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051332
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051332/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051332
Building REAL300025051333
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051333'
/scratch/stefan/7786831/working/building/REAL300025051333 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051333

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051333/0 /scratch/stefan/7786831/working/building/REAL300025051333 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 192)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/192
`/scratch/stefan/7786831/working/3D/192' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCN1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1=O)

`REAL300025051333.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051333.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051333/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051333 none CCCN1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 20, 6, 6, 6, 2, 2, 2, 1, 1, 1, 4, 7, 7, 7, 21, 31, 93, 93, 93, 93, 93, 1, 1, 6, 6, 6, 28, 28, 28, 28, 28, 20, 20, 6, 6, 6, 2, 4, 4, 7, 21, 21, 93, 1, 1, 1, 1, 6, 6] 201
rigid atoms, others: [8, 9, 10, 44, 45, 46, 47, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 48, 49])
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: REAL300025051333 none CCCN1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 5, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 15, 15, 15, 38, 56, 150, 150, 150, 150, 150, 6, 6, 1, 1, 1, 8, 8, 8, 7, 7, 5, 5, 1, 1, 1, 6, 9, 9, 15, 38, 38, 150, 6, 6, 6, 6, 1, 1] 201
rigid atoms, others: [34, 3, 4, 5, 6, 2, 48, 49, 35, 24, 25, 26, 36] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 350
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051333 none CCCN1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 150, 150, 150, 93, 93, 93, 93, 75, 47, 47, 26, 47, 13, 1, 1, 1, 1, 1, 1, 1, 93, 93, 150, 150, 150, 201, 201, 201, 201, 201, 201, 201, 150, 150, 150, 93, 75, 75, 47, 26, 26, 1, 93, 93, 93, 93, 150, 150] 201
rigid atoms, others: [43, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49])
total number of confs: 880
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051333 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051333
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051333/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051333
Building REAL300025051334
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051334'
/scratch/stefan/7786831/working/building/REAL300025051334 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051334

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051334/0 /scratch/stefan/7786831/working/building/REAL300025051334 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 193)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/193
`/scratch/stefan/7786831/working/3D/193' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)N1C=CN=C1)

`REAL300025051334.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051334.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051334/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051334 none CC(CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)N1C=CN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [138, 135, 78, 78, 78, 78, 67, 41, 41, 25, 41, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 138, 201, 201, 201, 201, 138, 138, 138, 138, 135, 135, 78, 67, 67, 41, 25, 25, 1, 78, 78, 78, 78, 201, 201, 201] 201
rigid atoms, others: [38, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 731
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051334 none CC(CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)N1C=CN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 8, 2, 2, 2, 1, 1, 1, 4, 6, 6, 6, 17, 27, 78, 78, 78, 78, 78, 1, 1, 16, 31, 31, 31, 31, 16, 16, 16, 16, 8, 8, 2, 4, 4, 6, 17, 17, 78, 1, 1, 1, 1, 31, 31, 31] 201
rigid atoms, others: [5, 6, 39, 40, 41, 42, 7, 19, 20] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45])
total number of confs: 247
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051334 none CC(CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)N1C=CN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 12, 31, 31, 31, 31, 49, 67, 67, 67, 113, 133, 201, 201, 201, 201, 201, 31, 31, 1, 1, 1, 1, 1, 6, 6, 6, 5, 12, 12, 31, 49, 49, 67, 113, 113, 201, 31, 31, 31, 31, 1, 1, 1] 201
rigid atoms, others: [1, 43, 44, 45, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 673
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051334 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051334
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051334/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051334
Building REAL300025051335
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051335'
/scratch/stefan/7786831/working/building/REAL300025051335 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051335

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051335/0 /scratch/stefan/7786831/working/building/REAL300025051335 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 194)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/194
`/scratch/stefan/7786831/working/3D/194' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(C)=N1)

`REAL300025051335.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051335.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051335/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051335 none CCN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 4, 4, 4, 2, 2, 2, 1, 1, 1, 4, 9, 9, 9, 27, 43, 117, 117, 117, 117, 117, 1, 1, 4, 4, 4, 11, 11, 11, 11, 11, 4, 2, 4, 4, 9, 27, 27, 117, 1, 1, 1, 1, 4, 4, 4] 201
rigid atoms, others: [39, 8, 9, 42, 7, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 43, 44, 45])
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: REAL300025051335 none CCN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 1, 1, 1, 1, 3, 3, 4, 4, 10, 21, 21, 21, 56, 80, 129, 129, 129, 129, 129, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 1, 4, 10, 10, 21, 56, 56, 129, 4, 4, 4, 4, 2, 2, 2] 201
rigid atoms, others: [1, 2, 3, 4, 5, 23, 24, 25, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 383
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051335 none CCN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 129, 129, 129, 117, 117, 117, 117, 102, 55, 55, 24, 55, 12, 1, 1, 1, 1, 1, 1, 1, 117, 117, 129, 129, 129, 201, 201, 201, 201, 201, 129, 117, 102, 102, 55, 24, 24, 1, 117, 117, 117, 117, 129, 129, 129] 201
rigid atoms, others: [38, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 913
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051335 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051335
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051335/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051335
Building REAL300025051336
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051336'
/scratch/stefan/7786831/working/building/REAL300025051336 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051336

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051336/0 /scratch/stefan/7786831/working/building/REAL300025051336 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 195)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/195
`/scratch/stefan/7786831/working/3D/195' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(Cl)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NN1C)

`REAL300025051336.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051336.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051336/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051336 none CC1=C(Cl)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 21, 21, 21, 79, 85, 159, 159, 159, 159, 159, 1, 1, 5, 5, 5, 5, 5, 5, 2, 4, 4, 21, 79, 79, 159, 1, 1, 1, 1, 5, 5, 5] 201
rigid atoms, others: [36, 37, 38, 7, 8, 9, 39, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42])
total number of confs: 420
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051336 none CC1=C(Cl)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 43, 43, 43, 127, 137, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 2, 2, 2, 5, 10, 10, 43, 127, 127, 201, 5, 5, 5, 5, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 23, 24, 25] set([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, 41, 42])
total number of confs: 619
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051336 none CC1=C(Cl)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 159, 159, 159, 159, 126, 69, 69, 32, 69, 13, 1, 1, 1, 1, 1, 1, 1, 159, 159, 201, 201, 201, 201, 201, 201, 159, 126, 126, 69, 32, 32, 1, 159, 159, 159, 159, 201, 201, 201] 201
rigid atoms, others: [35, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 673
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051336 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051336
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051336/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051336
Building REAL300025051337
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051337'
/scratch/stefan/7786831/working/building/REAL300025051337 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051337

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051337/0 /scratch/stefan/7786831/working/building/REAL300025051337 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 196)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/196
`/scratch/stefan/7786831/working/3D/196' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=NN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051337.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051337.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051337/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051337 none CC1=CC=NN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 14, 14, 14, 14, 9, 2, 2, 2, 1, 1, 1, 7, 20, 20, 20, 54, 63, 155, 155, 155, 155, 155, 1, 1, 14, 14, 14, 14, 14, 9, 9, 2, 7, 7, 20, 54, 54, 155, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 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: REAL300025051337 none CC1=CC=NN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 14, 14, 14, 14, 29, 57, 57, 57, 110, 119, 201, 201, 201, 201, 201, 14, 14, 2, 2, 2, 1, 1, 4, 4, 14, 29, 29, 57, 110, 110, 201, 14, 14, 14, 14] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 636
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051337 none CC1=CC=NN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 155, 155, 155, 155, 104, 51, 51, 30, 51, 13, 1, 1, 1, 1, 1, 1, 1, 155, 155, 201, 201, 201, 201, 201, 201, 201, 155, 104, 104, 51, 30, 30, 1, 155, 155, 155, 155] 201
rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 814
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051337 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051337
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051337/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051337
Building REAL300025051338
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051338'
/scratch/stefan/7786831/working/building/REAL300025051338 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051338

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051338/0 /scratch/stefan/7786831/working/building/REAL300025051338 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 197)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/197
`/scratch/stefan/7786831/working/3D/197' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1)

`REAL300025051338.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051338.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051338/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051338 none CCCN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 13, 4, 4, 4, 2, 2, 2, 1, 1, 1, 4, 14, 14, 14, 37, 45, 109, 109, 109, 109, 109, 1, 1, 4, 4, 18, 18, 18, 18, 18, 13, 13, 4, 2, 4, 4, 14, 37, 37, 109, 1, 1, 1, 1, 4] 201
rigid atoms, others: [43, 8, 9, 10, 23, 44, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 45])
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: REAL300025051338 none CCCN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 8, 1, 1, 1, 1, 1, 4, 4, 4, 4, 8, 21, 21, 21, 51, 60, 122, 122, 122, 122, 122, 4, 4, 1, 1, 12, 12, 12, 12, 12, 8, 8, 1, 4, 8, 8, 21, 51, 51, 122, 4, 4, 4, 4, 1] 201
rigid atoms, others: [33, 2, 3, 4, 5, 6, 45, 24, 25] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 360
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051338 none CCCN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 122, 122, 122, 109, 109, 109, 109, 93, 65, 65, 31, 65, 13, 1, 1, 1, 1, 1, 1, 1, 109, 109, 122, 122, 201, 201, 201, 201, 201, 201, 201, 122, 109, 93, 93, 65, 31, 31, 1, 109, 109, 109, 109, 122] 201
rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45])
total number of confs: 909
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051338 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051338
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051338/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051338
Building REAL300025051339
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051339'
/scratch/stefan/7786831/working/building/REAL300025051339 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051339

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051339/0 /scratch/stefan/7786831/working/building/REAL300025051339 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 198)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/198
`/scratch/stefan/7786831/working/3D/198' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(=O)N(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1)

`REAL300025051339.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051339.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051339/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051339 none CC1=CC(=O)N(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 10, 10, 9, 2, 2, 2, 1, 1, 1, 7, 23, 23, 23, 62, 81, 156, 156, 156, 156, 156, 1, 1, 10, 10, 10, 10, 10, 10, 9, 9, 2, 7, 7, 23, 62, 62, 156, 1, 1, 1, 1, 10, 10] 201
rigid atoms, others: [43, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45])
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: REAL300025051339 none CC1=CC(=O)N(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 10, 10, 10, 10, 23, 56, 56, 56, 111, 127, 201, 201, 201, 201, 201, 10, 10, 1, 1, 2, 2, 2, 1, 2, 2, 10, 23, 23, 56, 111, 111, 201, 10, 10, 10, 10, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 44, 45, 25, 26, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 602
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051339 none CC1=CC(=O)N(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 156, 156, 156, 156, 138, 84, 84, 45, 84, 13, 1, 1, 1, 1, 1, 1, 1, 156, 156, 201, 201, 201, 201, 201, 201, 201, 201, 156, 138, 138, 84, 45, 45, 1, 156, 156, 156, 156, 201, 201] 201
rigid atoms, others: [39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45])
total number of confs: 834
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051339 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051339
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051339/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051339
Building REAL300025051340
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051340'
/scratch/stefan/7786831/working/building/REAL300025051340 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051340

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051340/0 /scratch/stefan/7786831/working/building/REAL300025051340 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 199)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/199
`/scratch/stefan/7786831/working/3D/199' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NOC(C)=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051340.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051340.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051340/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051340 none CC1=NOC(C)=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 12, 1, 5, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 18, 18, 18, 18, 10, 2, 2, 2, 1, 1, 1, 6, 8, 8, 8, 17, 29, 83, 83, 83, 83, 83, 1, 1, 18, 18, 18, 18, 18, 18, 10, 10, 2, 6, 6, 8, 17, 17, 83, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 10, 11, 12, 44, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 214
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051340 none CC1=NOC(C)=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 12, 1, 5, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 18, 18, 18, 18, 33, 43, 43, 43, 87, 118, 201, 201, 201, 201, 201, 18, 18, 2, 2, 2, 2, 2, 2, 2, 2, 18, 33, 33, 43, 87, 87, 201, 18, 18, 18, 18] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 595
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051340 none CC1=NOC(C)=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 12, 1, 5, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 144, 83, 83, 83, 83, 72, 45, 45, 25, 45, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 201, 201, 201, 201, 201, 201, 144, 144, 83, 72, 72, 45, 25, 25, 1, 83, 83, 83, 83] 201
rigid atoms, others: [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, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 737
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051340 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051340
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051340/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051340
Building REAL300025051341
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051341'
/scratch/stefan/7786831/working/building/REAL300025051341 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051341

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051341/0 /scratch/stefan/7786831/working/building/REAL300025051341 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 200)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/200
`/scratch/stefan/7786831/working/3D/200' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NNC(C)=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051341.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051341.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051341/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051341 none CC1=NNC(C)=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 6, 21, 21, 21, 67, 84, 180, 180, 180, 180, 180, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 6, 6, 21, 67, 67, 180, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 459
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051341 none CC1=NNC(C)=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
121  conformations in input
total number of sets (complete confs): 121
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 24, 32, 32, 32, 60, 74, 121, 121, 121, 121, 121, 14, 14, 2, 2, 2, 1, 2, 2, 2, 2, 2, 14, 24, 24, 32, 60, 60, 121, 14, 14, 14, 14] 121
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 386
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051341 none CC1=NNC(C)=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 180, 180, 180, 180, 150, 68, 68, 30, 68, 13, 1, 1, 1, 1, 1, 1, 1, 180, 180, 201, 201, 201, 201, 201, 201, 201, 201, 201, 180, 150, 150, 68, 30, 30, 1, 180, 180, 180, 180] 201
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 797
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051341 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051341
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051341/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051341
Building REAL300025051342
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051342'
/scratch/stefan/7786831/working/building/REAL300025051342 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051342

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051342/0 /scratch/stefan/7786831/working/building/REAL300025051342 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 201)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/201
`/scratch/stefan/7786831/working/3D/201' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C(=O)NCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051342.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051342.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051342/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051342 none CC(C)(C)C(=O)NCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 197, 127, 127, 127, 127, 98, 62, 62, 30, 62, 13, 1, 1, 1, 1, 1, 1, 1, 127, 127, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 197, 197, 127, 98, 98, 62, 30, 30, 1, 127, 127, 127, 127] 201
rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48])
total number of confs: 809
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051342 none CC(C)(C)C(=O)NCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 19, 20, 20, 19, 19, 12, 2, 2, 2, 1, 1, 1, 6, 13, 13, 13, 34, 50, 127, 127, 127, 127, 127, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 19, 12, 12, 2, 6, 6, 13, 34, 34, 127, 1, 1, 1, 1] 201
rigid atoms, others: [10, 11, 12, 45, 46, 47, 48, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 337
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051342 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051342
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051342/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051342
Building REAL300025051343
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051343'
/scratch/stefan/7786831/working/building/REAL300025051343 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051343

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051343/0 /scratch/stefan/7786831/working/building/REAL300025051343 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 202)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/202
`/scratch/stefan/7786831/working/3D/202' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC(OCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051343.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051343.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051343/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051343 none CC1=CC=CC(OCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 23, 14, 23, 23, 10, 4, 2, 2, 2, 1, 1, 1, 4, 10, 10, 10, 19, 25, 65, 65, 65, 65, 65, 1, 1, 23, 23, 23, 23, 17, 23, 23, 4, 4, 2, 4, 4, 10, 19, 19, 65, 1, 1, 1, 1, 23] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46])
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: REAL300025051343 none CC1=CC=CC(OCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 12, 23, 23, 23, 23, 43, 64, 64, 64, 112, 137, 201, 201, 201, 201, 201, 23, 23, 1, 2, 2, 2, 1, 1, 1, 12, 12, 23, 43, 43, 64, 112, 112, 201, 23, 23, 23, 23, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 46, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 642
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051343 none CC1=CC=CC(OCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 174, 201, 201, 138, 81, 65, 65, 65, 65, 55, 43, 43, 36, 43, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 201, 201, 201, 201, 199, 201, 201, 81, 81, 65, 55, 55, 43, 36, 36, 1, 65, 65, 65, 65, 201] 201
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46])
total number of confs: 712
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051343 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051343
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051343/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051343
Building REAL300025051344
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051344'
/scratch/stefan/7786831/working/building/REAL300025051344 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051344

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051344/0 /scratch/stefan/7786831/working/building/REAL300025051344 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 203)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/203
`/scratch/stefan/7786831/working/3D/203' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(COC1=CC=CC(F)=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051344.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051344.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051344/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051344 none O=C(COC1=CC=CC(F)=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 4, 9, 24, 24, 24, 24, 24, 24, 1, 1, 1, 4, 9, 9, 9, 22, 28, 82, 82, 82, 82, 82, 1, 1, 4, 4, 24, 24, 24, 24, 2, 4, 4, 9, 22, 22, 82, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
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: REAL300025051344 none O=C(COC1=CC=CC(F)=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 41, 61, 61, 61, 108, 133, 201, 201, 201, 201, 201, 24, 24, 10, 10, 1, 1, 1, 1, 24, 41, 41, 61, 108, 108, 201, 24, 24, 24, 24] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051344 none O=C(COC1=CC=CC(F)=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [82, 82, 82, 102, 149, 201, 201, 201, 201, 201, 201, 82, 68, 54, 54, 43, 54, 13, 1, 1, 1, 1, 1, 1, 1, 82, 82, 102, 102, 201, 201, 201, 201, 82, 68, 68, 54, 43, 43, 1, 82, 82, 82, 82] 201
rigid atoms, others: [39, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 630
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051344 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051344
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051344/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051344
Building REAL300025051345
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051345'
/scratch/stefan/7786831/working/building/REAL300025051345 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051345

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051345/0 /scratch/stefan/7786831/working/building/REAL300025051345 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 204)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/204
`/scratch/stefan/7786831/working/3D/204' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCOC1=CC=CC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051345.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051345.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051345/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051345 none O=C(CCOC1=CC=CC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 10, 12, 28, 35, 35, 28, 35, 35, 1, 1, 1, 4, 8, 8, 8, 21, 31, 79, 79, 79, 79, 79, 1, 1, 10, 10, 12, 12, 35, 35, 28, 35, 35, 2, 4, 4, 8, 21, 21, 79, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
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: REAL300025051345 none O=C(CCOC1=CC=CC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [35, 15, 6, 4, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 51, 63, 63, 63, 115, 140, 201, 201, 201, 201, 201, 35, 35, 15, 15, 6, 6, 1, 1, 1, 1, 1, 35, 51, 51, 63, 115, 115, 201, 35, 35, 35, 35] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 679
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051345 none O=C(CCOC1=CC=CC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 160, 161, 201, 201, 201, 201, 201, 201, 79, 61, 44, 44, 24, 44, 12, 1, 1, 1, 1, 1, 1, 1, 79, 79, 160, 160, 161, 161, 201, 201, 201, 201, 201, 79, 61, 61, 44, 24, 24, 1, 79, 79, 79, 79] 201
rigid atoms, others: [42, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46])
total number of confs: 731
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051345 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051345
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051345/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051345
Building REAL300025051346
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051346'
/scratch/stefan/7786831/working/building/REAL300025051346 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051346

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051346/0 /scratch/stefan/7786831/working/building/REAL300025051346 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 205)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/205
`/scratch/stefan/7786831/working/3D/205' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(COC1=CC=CC=C1F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051346.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051346.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051346/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051346 none O=C(COC1=CC=CC=C1F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 1, 1, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 5, 16, 33, 33, 17, 33, 33, 33, 1, 1, 1, 3, 7, 7, 7, 19, 23, 56, 56, 56, 56, 56, 1, 1, 5, 5, 33, 33, 22, 33, 2, 3, 3, 7, 19, 19, 56, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
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: REAL300025051346 none O=C(COC1=CC=CC=C1F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 1, 1, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [33, 23, 11, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 53, 66, 66, 66, 118, 144, 201, 201, 201, 201, 201, 33, 33, 23, 23, 1, 1, 1, 1, 33, 53, 53, 66, 118, 118, 201, 33, 33, 33, 33] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051346 none O=C(COC1=CC=CC=C1F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 1, 1, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [56, 56, 56, 106, 182, 201, 201, 186, 201, 201, 201, 56, 52, 46, 46, 38, 46, 13, 1, 1, 1, 1, 1, 1, 1, 56, 56, 106, 106, 201, 201, 201, 201, 56, 52, 52, 46, 38, 38, 1, 56, 56, 56, 56] 201
rigid atoms, others: [39, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 681
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051346 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051346
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051346/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051346
Building REAL300025051347
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051347'
/scratch/stefan/7786831/working/building/REAL300025051347 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051347

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051347/0 /scratch/stefan/7786831/working/building/REAL300025051347 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 206)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/206
`/scratch/stefan/7786831/working/3D/206' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NOC(CCCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1)

`REAL300025051347.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051347.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051347/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051347 none CC1=NOC(CCCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [56, 56, 56, 56, 26, 14, 10, 2, 2, 2, 1, 1, 1, 3, 5, 5, 5, 12, 19, 54, 54, 54, 54, 54, 1, 1, 56, 56, 56, 56, 24, 25, 17, 17, 10, 10, 2, 3, 3, 5, 12, 12, 54, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 287
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051347 none CC1=NOC(CCCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 16, 27, 56, 56, 56, 56, 61, 65, 65, 65, 102, 123, 201, 201, 201, 201, 201, 56, 56, 1, 2, 2, 2, 8, 8, 16, 16, 27, 27, 56, 61, 61, 65, 102, 102, 201, 56, 56, 56, 56] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 671
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051347 none CC1=NOC(CCCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 117, 112, 54, 54, 54, 54, 43, 37, 37, 25, 37, 12, 1, 1, 1, 1, 1, 1, 1, 54, 54, 201, 201, 201, 201, 131, 138, 132, 132, 112, 112, 54, 43, 43, 37, 25, 25, 1, 54, 54, 54, 54] 201
rigid atoms, others: [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, 40, 41, 43, 44, 45, 46])
total number of confs: 771
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051347 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051347
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051347/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051347
Building REAL300025051348
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051348'
/scratch/stefan/7786831/working/building/REAL300025051348 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051348

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051348/0 /scratch/stefan/7786831/working/building/REAL300025051348 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 207)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/207
`/scratch/stefan/7786831/working/3D/207' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(NC(=O)C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1)

`REAL300025051348.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051348.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051348/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051348 none CC1=CC(NC(=O)C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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, 5, 5, 4, 4, 2, 4, 2, 2, 1, 1, 1, 7, 29, 29, 29, 88, 105, 192, 193, 193, 193, 193, 1, 1, 5, 5, 5, 5, 5, 5, 4, 2, 7, 7, 29, 88, 88, 193, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 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: REAL300025051348 none CC1=CC(NC(=O)C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 4, 5, 5, 5, 16, 42, 42, 42, 102, 117, 201, 201, 201, 201, 201, 5, 5, 1, 1, 2, 2, 2, 1, 2, 5, 16, 16, 42, 102, 102, 201, 5, 5, 5, 5] 201
rigid atoms, others: [0, 1, 2, 3, 4, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 577
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051348 none CC1=CC(NC(=O)C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 193, 201, 193, 193, 193, 125, 48, 48, 28, 48, 13, 1, 1, 1, 1, 1, 1, 1, 193, 193, 201, 201, 201, 201, 201, 201, 201, 193, 125, 125, 48, 28, 28, 1, 193, 193, 193, 193] 201
rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 744
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051348 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051348
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051348/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051348
Building REAL300025051349
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051349'
/scratch/stefan/7786831/working/building/REAL300025051349 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051349

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051349/0 /scratch/stefan/7786831/working/building/REAL300025051349 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 208)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/208
`/scratch/stefan/7786831/working/3D/208' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(=O)NC1=O)

`REAL300025051349.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051349.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051349/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051349 none CN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(=O)NC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 29, 29, 29, 90, 107, 197, 197, 197, 197, 197, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 29, 90, 90, 197, 1, 1, 1, 1, 4] 201
rigid atoms, others: [6, 38, 7, 8, 41, 39, 40, 20, 21] set([0, 1, 2, 3, 4, 5, 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, 36, 37, 42])
total number of confs: 533
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051349 none CN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(=O)NC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
201  conformations 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, 4, 4, 4, 4, 13, 41, 41, 41, 109, 125, 201, 201, 201, 201, 201, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 1, 4, 13, 13, 41, 109, 109, 201, 4, 4, 4, 4, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 42, 22, 23, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 597
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051349 none CN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(=O)NC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
201  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, 197, 197, 197, 133, 62, 62, 28, 62, 13, 1, 1, 1, 1, 1, 1, 1, 197, 197, 201, 201, 201, 201, 201, 201, 201, 201, 201, 197, 133, 133, 62, 28, 28, 1, 197, 197, 197, 197, 201] 201
rigid atoms, others: [37, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 742
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051349 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051349
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051349/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051349
Building REAL300025051350
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051350'
/scratch/stefan/7786831/working/building/REAL300025051350 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051350

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051350/0 /scratch/stefan/7786831/working/building/REAL300025051350 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 209)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/209
`/scratch/stefan/7786831/working/3D/209' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CNC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051350.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051350.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051350/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051350 none CC1=CNC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
193  conformations in input
total number of sets (complete confs): 193
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 6, 6, 2, 2, 2, 1, 1, 1, 4, 21, 21, 21, 89, 109, 170, 170, 170, 170, 170, 1, 1, 6, 6, 6, 6, 6, 6, 2, 4, 4, 21, 89, 89, 170, 1, 1, 1, 1] 193
rigid atoms, others: [37, 38, 39, 8, 9, 10, 40, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
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: REAL300025051350 none CC1=CNC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
193  conformations in input
total number of sets (complete confs): 193
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 13, 53, 53, 53, 128, 147, 193, 193, 193, 193, 193, 6, 6, 2, 2, 2, 1, 1, 1, 6, 13, 13, 53, 128, 128, 193, 6, 6, 6, 6] 193
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 593
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051350 none CC1=CNC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 193, 193, 170, 170, 170, 170, 153, 84, 84, 35, 84, 13, 1, 1, 1, 1, 1, 1, 1, 170, 170, 193, 193, 193, 193, 193, 193, 170, 153, 153, 84, 35, 35, 1, 170, 170, 170, 170] 193
rigid atoms, others: [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, 34, 35, 37, 38, 39, 40])
total number of confs: 678
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051350 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051350
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051350/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051350
Building REAL300025051351
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051351'
/scratch/stefan/7786831/working/building/REAL300025051351 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051351

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051351/0 /scratch/stefan/7786831/working/building/REAL300025051351 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 210)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/210
`/scratch/stefan/7786831/working/3D/210' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1)

`REAL300025051351.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051351.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051351/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051351 none CN1C=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 28, 28, 28, 98, 121, 201, 201, 201, 201, 201, 1, 1, 4, 4, 4, 4, 4, 4, 2, 7, 7, 28, 98, 98, 201, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 7, 8, 9, 39, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 548
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051351 none CN1C=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 11, 33, 33, 33, 103, 123, 201, 201, 201, 201, 201, 4, 4, 1, 2, 2, 2, 1, 1, 4, 11, 11, 33, 103, 103, 201, 4, 4, 4, 4] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 562
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051351 none CN1C=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 144, 54, 54, 30, 54, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 144, 144, 54, 30, 30, 1, 201, 201, 201, 201] 201
rigid atoms, others: [35, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39])
total number of confs: 767
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051351 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051351
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051351/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051351
Building REAL300025051352
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051352'
/scratch/stefan/7786831/working/building/REAL300025051352 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051352

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051352/0 /scratch/stefan/7786831/working/building/REAL300025051352 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 211)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/211
`/scratch/stefan/7786831/working/3D/211' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=CN=CC=C32)CC1)

`REAL300025051352.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051352.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051352/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051352 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=CN=CC=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 53, 60, 127, 127, 127, 127, 127, 5, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 53, 53, 127, 18, 5, 5, 3, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 42, 11, 12, 13, 44, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
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: REAL300025051352 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=CN=CC=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 13, 1, 1, 1, 1, 1, 1, 1, 56, 56, 104, 127, 127, 127, 127, 201, 201, 201, 201, 201, 201, 201, 201, 201, 127, 127, 32, 32, 1, 56, 104, 104, 127, 201, 201, 201, 201, 201, 201, 127, 127, 127, 127] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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])
total number of confs: 595
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051352 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=CN=CC=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 141, 152, 201, 201, 201, 201, 201, 23, 15, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 141, 141, 201, 66, 23, 23, 9, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15] 201
rigid atoms, others: [35, 36, 37, 38, 39, 40, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44])
total number of confs: 672
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051352 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051352
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051352/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051352
Building REAL300025051353
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051353'
/scratch/stefan/7786831/working/building/REAL300025051353 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051353

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051353/0 /scratch/stefan/7786831/working/building/REAL300025051353 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 212)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/212
`/scratch/stefan/7786831/working/3D/212' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC=CN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051353.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051353.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051353/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051353 none CC1=NC=CN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 18, 18, 18, 10, 2, 2, 2, 1, 1, 1, 6, 12, 12, 12, 29, 45, 128, 128, 128, 128, 128, 1, 1, 18, 18, 18, 18, 18, 10, 10, 2, 6, 6, 12, 29, 29, 128, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 297
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051353 none CC1=NC=CN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 18, 18, 18, 18, 30, 50, 50, 50, 101, 128, 201, 201, 201, 201, 201, 18, 18, 2, 2, 2, 1, 1, 5, 5, 18, 30, 30, 50, 101, 101, 201, 18, 18, 18, 18] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 619
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051353 none CC1=NC=CN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 191, 128, 128, 128, 128, 106, 53, 53, 28, 53, 13, 1, 1, 1, 1, 1, 1, 1, 128, 128, 201, 201, 201, 201, 201, 191, 191, 128, 106, 106, 53, 28, 28, 1, 128, 128, 128, 128] 201
rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 831
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051353 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051353/1 /scratch/stefan/7786831/working/building/REAL300025051353 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 213)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/213
`/scratch/stefan/7786831/working/3D/213' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=[NH+]C=CN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051353.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051353.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051353/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051353 none CC1=[NH+]C=CN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 6, 1, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [8, 8, 8, 8, 8, 8, 5, 2, 2, 2, 1, 1, 1, 4, 7, 7, 7, 18, 22, 33, 33, 33, 33, 33, 1, 1, 8, 8, 8, 8, 8, 5, 5, 2, 4, 4, 7, 18, 18, 33, 1, 1, 1, 1] 40
rigid atoms, others: [43, 40, 41, 10, 11, 12, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 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: REAL300025051353 none CC1=[NH+]C=CN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 6, 1, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 8, 10, 15, 15, 15, 28, 32, 40, 40, 40, 40, 40, 8, 8, 2, 2, 2, 1, 1, 4, 4, 8, 10, 10, 15, 28, 28, 40, 8, 8, 8, 8] 40
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29, 30] set([8, 9, 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])
total number of confs: 149
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051353 none CC1=[NH+]C=CN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 6, 1, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [40, 40, 40, 40, 40, 40, 37, 33, 33, 33, 33, 33, 30, 30, 18, 30, 12, 1, 1, 1, 1, 1, 1, 1, 33, 33, 40, 40, 40, 40, 40, 37, 37, 33, 33, 33, 30, 18, 18, 1, 33, 33, 33, 33] 40
rigid atoms, others: [39, 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, 40, 41, 42, 43])
total number of confs: 133
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051353 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051353
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051353/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051353/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051353
Building REAL300025051354
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051354'
/scratch/stefan/7786831/working/building/REAL300025051354 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051354

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051354/0 /scratch/stefan/7786831/working/building/REAL300025051354 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 214)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/214
`/scratch/stefan/7786831/working/3D/214' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CN1CCOCC1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051354.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051354.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051354/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051354 none CC(CN1CCOCC1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 10, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 2, 9, 19, 19, 19, 19, 19, 19, 2, 2, 1, 1, 1, 4, 9, 9, 9, 29, 45, 125, 125, 125, 125, 125, 1, 1, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 4, 4, 9, 29, 29, 125, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 48, 49, 50, 51, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 326
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051354 none CC(CN1CCOCC1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 10, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 19, 19, 19, 19, 37, 53, 53, 53, 100, 132, 201, 201, 201, 201, 201, 19, 19, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 19, 37, 37, 53, 100, 100, 201, 19, 19, 19, 19] 201
rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 39, 34, 40, 35, 36, 38, 37] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 626
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051354 none CC(CN1CCOCC1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 10, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [194, 125, 194, 201, 201, 201, 201, 201, 201, 125, 125, 125, 110, 64, 64, 31, 64, 13, 1, 1, 1, 1, 1, 1, 1, 125, 125, 194, 194, 194, 194, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 125, 110, 110, 64, 31, 31, 1, 125, 125, 125, 125] 201
rigid atoms, others: [47, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51])
total number of confs: 898
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051354 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051354/1 /scratch/stefan/7786831/working/building/REAL300025051354 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 215)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/215
`/scratch/stefan/7786831/working/3D/215' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C[NH+]1CCOCC1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051354.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051354.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051354/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051354 none CC(C[NH+]1CCOCC1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [6, 2, 6, 11, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 7, 14, 14, 14, 36, 51, 85, 85, 85, 85, 85, 1, 1, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 7, 7, 14, 36, 36, 85, 1, 1, 1, 1] 87
rigid atoms, others: [12, 13, 14, 49, 50, 51, 52, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 261
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: REAL300025051354 none CC(C[NH+]1CCOCC1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [5, 4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 11, 14, 22, 22, 22, 45, 58, 87, 87, 87, 87, 87, 11, 11, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 11, 14, 14, 22, 45, 45, 87, 11, 11, 11, 11] 87
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 39, 34, 40, 35, 41, 36, 38, 37] 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, 32, 33, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 250
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051354 none CC(C[NH+]1CCOCC1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [87, 85, 87, 87, 87, 87, 87, 87, 87, 87, 85, 85, 85, 78, 68, 68, 29, 68, 12, 1, 1, 1, 1, 1, 1, 1, 85, 85, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 85, 78, 78, 68, 29, 29, 1, 85, 85, 85, 85] 87
rigid atoms, others: [48, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52])
total number of confs: 312
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051354 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051354
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051354/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051354/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051354
Building REAL300025051355
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051355'
/scratch/stefan/7786831/working/building/REAL300025051355 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051355

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051355/0 /scratch/stefan/7786831/working/building/REAL300025051355 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 216)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/216
`/scratch/stefan/7786831/working/3D/216' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1)

`REAL300025051355.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051355.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051355/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051355 none CC1=CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 14, 14, 14, 5, 2, 2, 2, 1, 1, 1, 7, 17, 17, 17, 48, 64, 151, 151, 151, 151, 151, 1, 1, 14, 14, 14, 14, 14, 14, 14, 5, 5, 2, 7, 7, 17, 48, 48, 151, 1, 1, 1, 1, 14] 201
rigid atoms, others: [8, 9, 10, 43, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 44])
total number of confs: 368
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051355 none CC1=CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 14, 14, 14, 14, 30, 48, 48, 48, 90, 114, 201, 201, 201, 201, 201, 14, 14, 1, 1, 2, 2, 2, 1, 1, 7, 7, 14, 30, 30, 48, 90, 90, 201, 14, 14, 14, 14, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 584
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051355 none CC1=CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 174, 151, 151, 151, 151, 111, 57, 57, 28, 57, 13, 1, 1, 1, 1, 1, 1, 1, 151, 151, 201, 201, 201, 201, 201, 201, 201, 174, 174, 151, 111, 111, 57, 28, 28, 1, 151, 151, 151, 151, 201] 201
rigid atoms, others: [39, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44])
total number of confs: 768
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051355 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051355
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051355/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051355
Building REAL300025051356
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051356'
/scratch/stefan/7786831/working/building/REAL300025051356 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051356

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051356/0 /scratch/stefan/7786831/working/building/REAL300025051356 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 217)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/217
`/scratch/stefan/7786831/working/3D/217' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CN1)

`REAL300025051356.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051356.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051356/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051356 none NC(=O)C1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CN1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 6, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 19, 19, 19, 70, 81, 139, 139, 139, 139, 139, 1, 1, 5, 5, 5, 5, 5, 2, 4, 4, 19, 70, 70, 139, 1, 1, 1, 1, 5, 5] 201
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41])
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: REAL300025051356 none NC(=O)C1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CN1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 6, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 5, 5, 13, 56, 56, 56, 138, 150, 201, 201, 201, 201, 201, 5, 5, 1, 1, 2, 2, 1, 5, 13, 13, 56, 138, 138, 201, 5, 5, 5, 5, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 40, 41, 24, 25, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 648
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051356 none NC(=O)C1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CN1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 6, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 139, 139, 139, 139, 114, 59, 59, 25, 59, 13, 1, 1, 1, 1, 1, 1, 1, 139, 139, 201, 201, 201, 201, 201, 139, 114, 114, 59, 25, 25, 1, 139, 139, 139, 139, 201, 201] 201
rigid atoms, others: [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, 33, 34, 36, 37, 38, 39, 40, 41])
total number of confs: 641
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051356 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051356
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051356/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051356
Building REAL300025051357
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051357'
/scratch/stefan/7786831/working/building/REAL300025051357 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051357

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051357/0 /scratch/stefan/7786831/working/building/REAL300025051357 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 218)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/218
`/scratch/stefan/7786831/working/3D/218' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051357.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051357.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051357/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051357 none CCN1C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 7, 17, 17, 17, 45, 52, 137, 137, 137, 137, 137, 1, 1, 10, 10, 10, 10, 10, 5, 5, 5, 2, 7, 7, 17, 45, 45, 137, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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: REAL300025051357 none CCN1C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 15, 34, 34, 34, 73, 82, 151, 151, 151, 151, 151, 5, 5, 4, 4, 4, 4, 4, 1, 1, 1, 5, 15, 15, 34, 73, 73, 151, 5, 5, 5, 5] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 447
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051357 none CCN1C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 151, 151, 151, 151, 151, 137, 137, 137, 137, 98, 46, 46, 22, 46, 11, 1, 1, 1, 1, 1, 1, 1, 137, 137, 201, 201, 201, 201, 201, 151, 151, 151, 137, 98, 98, 46, 22, 22, 1, 137, 137, 137, 137] 201
rigid atoms, others: [39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 843
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051357 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051357
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051357/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051357
Building REAL300025051358
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051358'
/scratch/stefan/7786831/working/building/REAL300025051358 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051358

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051358/0 /scratch/stefan/7786831/working/building/REAL300025051358 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 219)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/219
`/scratch/stefan/7786831/working/3D/219' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)N1C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051358.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051358.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051358/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051358 none CC(C)N1C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 5, 10, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 6, 17, 17, 17, 50, 65, 159, 159, 159, 159, 159, 1, 1, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 2, 6, 6, 17, 50, 50, 159, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 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: REAL300025051358 none CC(C)N1C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 16, 34, 34, 34, 93, 112, 201, 201, 201, 201, 201, 5, 5, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 5, 16, 16, 34, 93, 93, 201, 5, 5, 5, 5] 201
rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 8, 7, 35] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 580
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051358 none CC(C)N1C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 159, 159, 159, 159, 109, 53, 53, 25, 53, 13, 1, 1, 1, 1, 1, 1, 1, 159, 159, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 159, 109, 109, 53, 25, 25, 1, 159, 159, 159, 159] 201
rigid atoms, others: [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, 40, 41, 43, 44, 45, 46])
total number of confs: 686
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051358 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051358
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051358/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051358
Building REAL300025051359
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051359'
/scratch/stefan/7786831/working/building/REAL300025051359 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051359

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051359/0 /scratch/stefan/7786831/working/building/REAL300025051359 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 220)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/220
`/scratch/stefan/7786831/working/3D/220' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C(Cl)N=CS2)CC1)

`REAL300025051359.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051359.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051359/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051359 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C(Cl)N=CS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 16, 8, 1, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 20, 58, 71, 122, 122, 122, 122, 122, 5, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 1, 1, 58, 58, 122, 20, 5, 5, 3, 10, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 340
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051359 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C(Cl)N=CS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 16, 8, 1, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [63, 31, 13, 1, 1, 1, 1, 1, 1, 1, 63, 63, 105, 122, 122, 122, 122, 201, 201, 201, 201, 201, 122, 122, 31, 31, 1, 63, 105, 105, 122, 201, 122, 122, 122, 122] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 586
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051359 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C(Cl)N=CS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 16, 8, 1, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [59, 59, 59, 131, 154, 201, 201, 201, 201, 201, 17, 10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 131, 131, 201, 59, 17, 17, 6, 1, 10, 10, 10, 10] 201
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 641
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051359 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051359
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051359/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051359
Building REAL300025051360
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051360'
/scratch/stefan/7786831/working/building/REAL300025051360 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051360

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051360/0 /scratch/stefan/7786831/working/building/REAL300025051360 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 221)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/221
`/scratch/stefan/7786831/working/3D/221' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C=C(Cl)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051360.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051360.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051360/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051360 none CCN1C=C(Cl)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 5, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 7, 18, 18, 18, 44, 52, 141, 141, 141, 141, 141, 1, 1, 10, 10, 10, 10, 10, 5, 5, 2, 7, 7, 18, 44, 44, 141, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 10, 11, 12, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 347
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051360 none CCN1C=C(Cl)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 16, 36, 36, 36, 80, 90, 164, 164, 164, 164, 164, 5, 5, 4, 4, 4, 4, 4, 1, 1, 5, 16, 16, 36, 80, 80, 164, 5, 5, 5, 5] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 483
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051360 none CCN1C=C(Cl)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 164, 164, 164, 164, 164, 164, 141, 141, 141, 141, 101, 48, 48, 23, 48, 12, 1, 1, 1, 1, 1, 1, 1, 141, 141, 201, 201, 201, 201, 201, 164, 164, 141, 101, 101, 48, 23, 23, 1, 141, 141, 141, 141] 201
rigid atoms, others: [39, 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, 40, 41, 42, 43])
total number of confs: 789
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051360 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051360
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051360/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051360
Building REAL300025051361
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051361'
/scratch/stefan/7786831/working/building/REAL300025051361 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051361

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051361/0 /scratch/stefan/7786831/working/building/REAL300025051361 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 222)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/222
`/scratch/stefan/7786831/working/3D/222' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCCOC2)CC1)

`REAL300025051361.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051361.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051361/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051361 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCCOC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 14, 32, 35, 75, 75, 75, 75, 75, 5, 1, 1, 1, 3, 3, 3, 19, 47, 47, 47, 47, 45, 1, 1, 32, 32, 75, 14, 5, 5, 3, 19, 19, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1] 201
rigid atoms, others: [11, 44, 43, 12, 13, 46, 45, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
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: REAL300025051361 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCCOC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [36, 24, 13, 1, 1, 1, 1, 1, 1, 1, 36, 36, 65, 75, 75, 75, 75, 170, 201, 201, 201, 201, 201, 75, 75, 24, 24, 1, 36, 65, 65, 75, 170, 170, 201, 201, 201, 201, 201, 201, 201, 201, 201, 75, 75, 75, 75] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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, 45, 46])
total number of confs: 811
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051361 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCCOC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [134, 134, 134, 191, 194, 201, 201, 201, 201, 201, 63, 47, 27, 27, 8, 27, 1, 1, 1, 1, 1, 1, 1, 47, 47, 191, 191, 201, 134, 63, 63, 27, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46])
total number of confs: 796
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051361 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051361
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051361/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051361
Building REAL300025051362
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051362'
/scratch/stefan/7786831/working/building/REAL300025051362 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051362

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051362/0 /scratch/stefan/7786831/working/building/REAL300025051362 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 223)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/223
`/scratch/stefan/7786831/working/3D/223' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC=CCC2)CC1)

`REAL300025051362.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051362.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051362/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051362 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC=CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 21, 21, 65, 75, 147, 147, 147, 147, 147, 5, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 1, 1, 65, 65, 147, 21, 5, 5, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1] 201
rigid atoms, others: [11, 44, 43, 12, 13, 46, 45, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 401
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051362 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC=CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [66, 31, 12, 1, 1, 1, 1, 1, 1, 1, 66, 66, 120, 147, 147, 147, 147, 201, 201, 201, 201, 201, 201, 147, 147, 31, 31, 1, 66, 120, 120, 147, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 147, 147, 147, 147] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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, 45, 46])
total number of confs: 746
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051362 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC=CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [63, 63, 63, 142, 151, 201, 201, 201, 201, 201, 20, 15, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 15, 15, 142, 142, 201, 63, 20, 20, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 43, 44, 45, 46])
total number of confs: 652
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051362 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051362
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051362/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051362
Building REAL300025051363
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051363'
/scratch/stefan/7786831/working/building/REAL300025051363 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051363

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051363/0 /scratch/stefan/7786831/working/building/REAL300025051363 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 224)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/224
`/scratch/stefan/7786831/working/3D/224' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051363.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051363.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051363/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051363 none NC(=O)C1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 18, 18, 18, 40, 48, 67, 67, 67, 67, 67, 1, 1, 5, 5, 5, 5, 5, 2, 4, 4, 18, 40, 40, 67, 1, 1, 1, 1, 5] 77
rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42])
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: REAL300025051363 none NC(=O)C1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 5, 5, 5, 5, 11, 32, 32, 32, 54, 62, 77, 77, 77, 77, 77, 5, 5, 1, 2, 2, 1, 1, 5, 11, 11, 32, 54, 54, 77, 5, 5, 5, 5, 1] 77
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 42, 26, 29, 30] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 256
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051363 none NC(=O)C1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 67, 67, 67, 67, 63, 51, 51, 29, 51, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 77, 77, 77, 77, 77, 67, 63, 63, 51, 29, 29, 1, 67, 67, 67, 67, 77] 77
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 257
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051363 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051363
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051363/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051363
Building REAL300025051364
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051364'
/scratch/stefan/7786831/working/building/REAL300025051364 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051364

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051364/0 /scratch/stefan/7786831/working/building/REAL300025051364 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 225)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/225
`/scratch/stefan/7786831/working/3D/225' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCS(=O)(=O)N2)CC1)

`REAL300025051364.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051364.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051364/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051364 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCS(=O)(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 14, 11, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 76, 91, 164, 164, 164, 164, 164, 5, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 1, 1, 76, 76, 164, 24, 5, 5, 3, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 451
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051364 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCS(=O)(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 14, 11, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [75, 34, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 126, 164, 164, 164, 164, 201, 201, 201, 201, 201, 201, 164, 164, 34, 34, 1, 75, 126, 126, 164, 201, 201, 201, 201, 201, 201, 164, 164, 164, 164] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 732
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051364 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCS(=O)(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 14, 11, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [82, 82, 82, 146, 162, 201, 201, 201, 201, 201, 26, 15, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 15, 15, 146, 146, 201, 82, 26, 26, 10, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41])
total number of confs: 674
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051364 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051364
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051364/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051364
Building REAL300025051365
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051365'
/scratch/stefan/7786831/working/building/REAL300025051365 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051365

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051365/0 /scratch/stefan/7786831/working/building/REAL300025051365 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 226)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/226
`/scratch/stefan/7786831/working/3D/226' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1)

`REAL300025051365.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051365.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051365/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051365 none CC1=NC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 31, 31, 31, 99, 116, 201, 201, 201, 201, 201, 1, 1, 4, 4, 4, 4, 4, 4, 2, 7, 7, 31, 99, 99, 201, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 40, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 547
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051365 none CC1=NC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 13, 41, 41, 41, 110, 126, 201, 201, 201, 201, 201, 4, 4, 1, 2, 2, 2, 1, 1, 4, 13, 13, 41, 110, 110, 201, 4, 4, 4, 4] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 584
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051365 none CC1=NC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 129, 58, 58, 29, 58, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 129, 129, 58, 29, 29, 1, 201, 201, 201, 201] 201
rigid atoms, others: [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, 34, 35, 37, 38, 39, 40])
total number of confs: 756
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051365 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051365
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051365/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051365
Building REAL300025051366
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051366'
/scratch/stefan/7786831/working/building/REAL300025051366 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051366

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051366/0 /scratch/stefan/7786831/working/building/REAL300025051366 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 227)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/227
`/scratch/stefan/7786831/working/3D/227' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC(C)=C1F)

`REAL300025051366.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051366.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051366/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051366 none CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC(C)=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 5, 1, 15, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 3, 2, 2, 2, 1, 1, 1, 4, 21, 21, 21, 84, 99, 146, 146, 146, 146, 146, 1, 1, 3, 3, 3, 2, 2, 3, 3, 3, 3, 2, 4, 4, 21, 84, 84, 146, 1, 1, 1, 1, 3, 3, 3, 3] 201
rigid atoms, others: [6, 38, 7, 8, 41, 39, 40, 20, 21] set([0, 1, 2, 3, 4, 5, 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, 36, 37, 42, 43, 44, 45])
total number of confs: 418
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051366 none CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC(C)=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 5, 1, 15, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
167  conformations in input
total number of sets (complete confs): 167
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 53, 53, 53, 107, 130, 167, 167, 167, 167, 167, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2, 1, 5, 13, 13, 53, 107, 107, 167, 5, 5, 5, 5, 1, 2, 2, 2] 167
rigid atoms, others: [0, 1, 2, 3, 4, 42, 22, 23, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45])
total number of confs: 516
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051366 none CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC(C)=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 5, 1, 15, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 146, 146, 146, 146, 125, 67, 67, 30, 67, 13, 1, 1, 1, 1, 1, 1, 1, 146, 146, 201, 201, 201, 146, 146, 201, 201, 201, 201, 146, 125, 125, 67, 30, 30, 1, 146, 146, 146, 146, 201, 201, 201, 201] 201
rigid atoms, others: [37, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 833
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051366 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051366
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051366/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051366
Building REAL300025051367
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051367'
/scratch/stefan/7786831/working/building/REAL300025051367 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051367

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051367/0 /scratch/stefan/7786831/working/building/REAL300025051367 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 228)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/228
`/scratch/stefan/7786831/working/3D/228' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC[NH+]1CCCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051367.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051367.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051367/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051367 none O=C(CCC[NH+]1CCCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [2, 2, 2, 5, 6, 8, 12, 12, 12, 12, 12, 12, 1, 1, 1, 3, 7, 7, 7, 13, 16, 31, 31, 31, 31, 31, 1, 1, 5, 5, 7, 7, 7, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 3, 3, 7, 13, 13, 31, 1, 1, 1, 1] 39
rigid atoms, others: [12, 13, 14, 51, 52, 53, 54, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 130
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: REAL300025051367 none O=C(CCC[NH+]1CCCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [12, 8, 4, 3, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 16, 16, 16, 24, 27, 39, 39, 39, 39, 39, 12, 12, 8, 8, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 16, 24, 24, 39, 12, 12, 12, 12] 39
rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 40, 43, 41, 36, 38, 42, 39, 37] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 133
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051367 none O=C(CCC[NH+]1CCCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [31, 31, 31, 36, 36, 37, 39, 39, 39, 39, 39, 39, 31, 29, 21, 21, 15, 21, 11, 1, 1, 1, 1, 1, 1, 1, 31, 31, 36, 36, 36, 36, 37, 37, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 31, 29, 29, 21, 15, 15, 1, 31, 31, 31, 31] 39
rigid atoms, others: [50, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54])
total number of confs: 157
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051367 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051367
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051367/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051367
Building REAL300025051368
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051368'
/scratch/stefan/7786831/working/building/REAL300025051368 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051368

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051368/0 /scratch/stefan/7786831/working/building/REAL300025051368 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 229)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/229
`/scratch/stefan/7786831/working/3D/229' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)C(=O)NCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051368.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051368.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051368/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051368 none CCC(C)C(=O)NCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [55, 55, 38, 55, 38, 38, 38, 34, 34, 34, 34, 33, 33, 33, 27, 33, 12, 1, 1, 1, 1, 1, 1, 1, 34, 34, 55, 55, 55, 55, 55, 55, 55, 55, 55, 38, 38, 38, 34, 33, 33, 33, 27, 27, 1, 34, 34, 34, 34] 55
rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48])
total number of confs: 224
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051368 none CCC(C)C(=O)NCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [12, 10, 5, 10, 5, 5, 4, 2, 2, 2, 1, 1, 1, 6, 10, 10, 10, 16, 20, 34, 34, 34, 34, 34, 1, 1, 12, 12, 12, 12, 12, 10, 10, 10, 10, 5, 4, 4, 2, 6, 6, 10, 16, 16, 34, 1, 1, 1, 1] 55
rigid atoms, others: [10, 11, 12, 45, 46, 47, 48, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 141
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051368 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051368
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051368/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051368
Building REAL300025051369
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051369'
/scratch/stefan/7786831/working/building/REAL300025051369 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051369

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051369/0 /scratch/stefan/7786831/working/building/REAL300025051369 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 230)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/230
`/scratch/stefan/7786831/working/3D/230' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCN1CCCC1=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051369.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051369.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051369/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051369 none O=C(CCN1CCCC1=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 10, 15, 20, 20, 20, 20, 20, 1, 1, 1, 4, 7, 7, 7, 25, 43, 124, 124, 124, 124, 124, 1, 1, 10, 10, 15, 15, 20, 20, 20, 20, 20, 20, 2, 4, 4, 7, 25, 25, 124, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 312
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051369 none O=C(CCN1CCCC1=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 10, 7, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 31, 47, 47, 47, 106, 142, 201, 201, 201, 201, 201, 20, 20, 10, 10, 7, 7, 1, 1, 1, 1, 1, 1, 20, 31, 31, 47, 106, 106, 201, 20, 20, 20, 20] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 35, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 638
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051369 none O=C(CCN1CCCC1=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [124, 124, 124, 199, 201, 201, 201, 201, 201, 201, 124, 101, 60, 60, 26, 60, 13, 1, 1, 1, 1, 1, 1, 1, 124, 124, 199, 199, 201, 201, 201, 201, 201, 201, 201, 201, 124, 101, 101, 60, 26, 26, 1, 124, 124, 124, 124] 201
rigid atoms, others: [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, 40, 41, 43, 44, 45, 46])
total number of confs: 885
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051369 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051369
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051369/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051369
Building REAL300025051370
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051370'
/scratch/stefan/7786831/working/building/REAL300025051370 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051370

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051370/0 /scratch/stefan/7786831/working/building/REAL300025051370 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 231)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/231
`/scratch/stefan/7786831/working/3D/231' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNS(=O)(=O)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051370.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051370.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051370/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051370 none CNS(=O)(=O)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 14, 11, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 182, 201, 201, 175, 175, 175, 175, 163, 97, 97, 35, 97, 13, 1, 1, 1, 1, 1, 1, 1, 175, 175, 201, 201, 201, 201, 182, 182, 175, 163, 163, 97, 35, 35, 1, 175, 175, 175, 175] 201
rigid atoms, others: [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, 34, 35, 37, 38, 39, 40])
total number of confs: 817
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051370 none CNS(=O)(=O)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 14, 11, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 9, 5, 9, 9, 2, 2, 2, 1, 1, 1, 4, 9, 9, 9, 38, 74, 175, 175, 175, 175, 175, 1, 1, 17, 17, 17, 17, 5, 5, 2, 4, 4, 9, 38, 38, 175, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 40, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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/7786831/working/building/REAL300025051370 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051370
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051370/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051370
Building REAL300025051371
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051371'
/scratch/stefan/7786831/working/building/REAL300025051371 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051371

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051371/0 /scratch/stefan/7786831/working/building/REAL300025051371 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 232)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/232
`/scratch/stefan/7786831/working/3D/232' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCS(=O)(=O)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051371.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051371.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051371/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051371 none CCCS(=O)(=O)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 200, 193, 200, 200, 176, 176, 176, 176, 149, 89, 89, 34, 89, 13, 1, 1, 1, 1, 1, 1, 1, 176, 176, 201, 201, 201, 201, 201, 201, 201, 193, 193, 176, 149, 149, 89, 34, 34, 1, 176, 176, 176, 176] 201
rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 825
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051371 none CCCS(=O)(=O)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 15, 9, 6, 9, 9, 2, 2, 2, 1, 1, 1, 5, 12, 12, 12, 49, 86, 176, 176, 176, 176, 176, 1, 1, 17, 17, 17, 17, 17, 15, 15, 6, 6, 2, 5, 5, 12, 49, 49, 176, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 458
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051371 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051371
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051371/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051371
Building REAL300025051372
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051372'
/scratch/stefan/7786831/working/building/REAL300025051372 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051372

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051372/0 /scratch/stefan/7786831/working/building/REAL300025051372 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 233)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/233
`/scratch/stefan/7786831/working/3D/233' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)S(=O)(=O)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051372.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051372.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051372/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051372 none CC(C)S(=O)(=O)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 200, 201, 201, 174, 174, 174, 174, 149, 91, 91, 33, 91, 13, 1, 1, 1, 1, 1, 1, 1, 174, 174, 201, 201, 201, 201, 201, 201, 201, 200, 200, 174, 149, 149, 91, 33, 33, 1, 174, 174, 174, 174] 201
rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 812
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051372 none CC(C)S(=O)(=O)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 9, 14, 6, 9, 9, 2, 2, 2, 1, 1, 1, 5, 11, 11, 11, 45, 81, 174, 174, 174, 174, 174, 1, 1, 14, 14, 14, 14, 14, 14, 14, 6, 6, 2, 5, 5, 11, 45, 45, 174, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 432
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051372 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051372
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051372/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051372
Building REAL300025051373
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051373'
/scratch/stefan/7786831/working/building/REAL300025051373 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051373

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051373/0 /scratch/stefan/7786831/working/building/REAL300025051373 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 234)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/234
`/scratch/stefan/7786831/working/3D/234' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3C=CC=CN23)CC1)

`REAL300025051373.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051373.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051373/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051373 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3C=CC=CN23)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 26, 26, 80, 92, 181, 181, 181, 181, 181, 5, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 80, 80, 181, 26, 5, 5, 3, 8, 8, 8, 8, 8, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 458
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051373 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3C=CC=CN23)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 30, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 132, 181, 181, 181, 181, 201, 201, 201, 201, 201, 201, 201, 201, 181, 181, 30, 30, 1, 61, 132, 132, 181, 201, 201, 201, 201, 201, 181, 181, 181, 181] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 710
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051373 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3C=CC=CN23)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [59, 59, 59, 135, 144, 201, 201, 201, 201, 201, 13, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 135, 135, 201, 59, 13, 13, 5, 1, 1, 1, 1, 1, 8, 8, 8, 8] 201
rigid atoms, others: [34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42])
total number of confs: 636
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051373 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051373
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051373/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051373
Building REAL300025051374
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051374'
/scratch/stefan/7786831/working/building/REAL300025051374 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051374

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051374/0 /scratch/stefan/7786831/working/building/REAL300025051374 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 235)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/235
`/scratch/stefan/7786831/working/3D/235' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2(F)CCCC2)CC1)

`REAL300025051374.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051374.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051374/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051374 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2(F)CCCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 27, 73, 85, 178, 178, 178, 178, 178, 6, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 1, 1, 73, 73, 178, 27, 6, 6, 3, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 455
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051374 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2(F)CCCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [62, 33, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 138, 178, 178, 178, 178, 201, 201, 201, 201, 201, 178, 178, 33, 33, 1, 62, 138, 138, 178, 201, 201, 201, 201, 201, 201, 201, 201, 178, 178, 178, 178] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 767
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051374 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2(F)CCCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [64, 64, 64, 133, 143, 201, 201, 201, 201, 201, 18, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 133, 133, 201, 64, 18, 18, 7, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41, 42])
total number of confs: 645
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051374 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051374
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051374/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051374
Building REAL300025051375
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051375'
/scratch/stefan/7786831/working/building/REAL300025051375 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051375

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051375/0 /scratch/stefan/7786831/working/building/REAL300025051375 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 236)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/236
`/scratch/stefan/7786831/working/3D/236' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1)

`REAL300025051375.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051375.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051375/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051375 none CN(C)CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 3, 3, 2, 2, 2, 1, 1, 1, 6, 14, 14, 14, 44, 48, 131, 131, 131, 131, 131, 1, 1, 3, 3, 15, 15, 15, 15, 15, 15, 11, 11, 3, 2, 6, 6, 14, 44, 44, 131, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 46, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
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: REAL300025051375 none CN(C)CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 7, 12, 1, 1, 1, 1, 1, 3, 3, 3, 3, 7, 16, 16, 16, 48, 52, 137, 137, 137, 137, 137, 3, 3, 1, 1, 12, 12, 12, 12, 12, 12, 7, 7, 1, 3, 7, 7, 16, 48, 48, 137, 3, 3, 3, 3] 201
rigid atoms, others: [35, 4, 5, 6, 7, 3, 25, 26] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 359
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051375 none CN(C)CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 137, 137, 131, 131, 131, 131, 91, 40, 40, 21, 40, 12, 1, 1, 1, 1, 1, 1, 1, 131, 131, 137, 137, 201, 201, 201, 201, 201, 201, 201, 201, 137, 131, 91, 91, 40, 21, 21, 1, 131, 131, 131, 131] 201
rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46])
total number of confs: 850
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051375 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051375/1 /scratch/stefan/7786831/working/building/REAL300025051375 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 237)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/237
`/scratch/stefan/7786831/working/3D/237' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+](C)CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1)

`REAL300025051375.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051375.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051375/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051375 none C[NH+](C)CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
10  conformations in input
total number of sets (complete confs): 10
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 1, 1, 1, 3, 4, 4, 4, 7, 8, 10, 10, 10, 10, 10, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 3, 3, 4, 7, 7, 10, 1, 1, 1, 1] 10
rigid atoms, others: [44, 10, 11, 12, 45, 46, 47, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
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: REAL300025051375 none C[NH+](C)CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
10  conformations in input
total number of sets (complete confs): 10
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 4, 4, 4, 7, 8, 10, 10, 10, 10, 10, 2, 2, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 3, 3, 4, 7, 7, 10, 2, 2, 2, 2] 10
rigid atoms, others: [36, 5, 6, 7, 8, 4, 26, 27] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 45
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051375 none C[NH+](C)CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
10  conformations in input
total number of sets (complete confs): 10
using default count positions algorithm for smaller data
unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 9, 8, 9, 6, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 8, 8, 1, 10, 10, 10, 10] 10
rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47])
total number of confs: 29
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051375 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051375
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051375/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051375/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051375
Building REAL300025051376
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051376'
/scratch/stefan/7786831/working/building/REAL300025051376 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051376

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051376/0 /scratch/stefan/7786831/working/building/REAL300025051376 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 238)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/238
`/scratch/stefan/7786831/working/3D/238' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C(=O)NCC(F)F)CC1)

`REAL300025051376.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051376.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051376/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051376 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C(=O)NCC(F)F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 15, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
126  conformations in input
total number of sets (complete confs): 126
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 20, 22, 44, 44, 44, 44, 44, 4, 1, 1, 1, 3, 3, 3, 13, 12, 12, 46, 63, 63, 1, 1, 20, 20, 44, 11, 4, 4, 3, 13, 46, 46, 63, 1, 1, 1, 1] 126
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 354
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051376 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C(=O)NCC(F)F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 15, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
126  conformations in input
total number of sets (complete confs): 126
using faster count positions algorithm for large data
unique positions, atoms: [30, 17, 12, 1, 1, 1, 1, 1, 1, 1, 30, 30, 44, 44, 44, 44, 44, 71, 71, 71, 126, 126, 126, 44, 44, 17, 17, 1, 30, 44, 44, 44, 71, 126, 126, 126, 44, 44, 44, 44] 126
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 515
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051376 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051376
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051376/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051376
Building REAL300025051377
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051377'
/scratch/stefan/7786831/working/building/REAL300025051377 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051377

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051377/0 /scratch/stefan/7786831/working/building/REAL300025051377 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 239)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/239
`/scratch/stefan/7786831/working/3D/239' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN(CCF)N=C2)CC1)

`REAL300025051377.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051377.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051377/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051377 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN(CCF)N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 15, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 12, 38, 45, 112, 112, 112, 112, 112, 4, 1, 1, 1, 3, 3, 3, 7, 7, 7, 24, 34, 7, 7, 1, 1, 38, 38, 112, 12, 4, 4, 3, 7, 24, 24, 34, 34, 7, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 390
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051377 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN(CCF)N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 15, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [67, 34, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 99, 112, 112, 112, 112, 144, 144, 144, 201, 201, 144, 144, 112, 112, 34, 34, 1, 67, 99, 99, 112, 144, 201, 201, 201, 201, 144, 112, 112, 112, 112] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 791
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051377 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN(CCF)N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 15, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 26, 26, 64, 72, 144, 144, 144, 144, 144, 10, 7, 5, 5, 1, 5, 1, 1, 1, 1, 6, 9, 1, 1, 7, 7, 64, 64, 144, 26, 10, 10, 5, 1, 6, 6, 9, 9, 1, 7, 7, 7, 7] 201
rigid atoms, others: [33, 38, 14, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 412
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051377 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051377
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051377/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051377
Building REAL300025051378
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051378'
/scratch/stefan/7786831/working/building/REAL300025051378 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051378

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051378/0 /scratch/stefan/7786831/working/building/REAL300025051378 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 240)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/240
`/scratch/stefan/7786831/working/3D/240' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051378.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051378.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051378/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051378 none CC1=CC(C)=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 28, 28, 28, 90, 103, 196, 197, 197, 197, 197, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 28, 90, 90, 197, 1, 1, 1, 1, 4] 201
rigid atoms, others: [43, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44])
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: REAL300025051378 none CC1=CC(C)=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 15, 48, 48, 48, 119, 134, 200, 201, 201, 201, 201, 4, 4, 1, 2, 2, 2, 1, 2, 2, 2, 4, 15, 15, 48, 119, 119, 201, 4, 4, 4, 4, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 25, 29] set([8, 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])
total number of confs: 618
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051378 none CC1=CC(C)=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 197, 197, 197, 197, 126, 56, 56, 29, 56, 13, 1, 1, 1, 1, 1, 1, 1, 197, 197, 201, 201, 201, 201, 201, 201, 201, 201, 197, 126, 126, 56, 29, 29, 1, 197, 197, 197, 197, 201] 201
rigid atoms, others: [39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44])
total number of confs: 727
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051378 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051378
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051378/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051378
Building REAL300025051379
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051379'
/scratch/stefan/7786831/working/building/REAL300025051379 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051379

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051379/0 /scratch/stefan/7786831/working/building/REAL300025051379 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 241)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/241
`/scratch/stefan/7786831/working/3D/241' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=NC=NN32)CC1)

`REAL300025051379.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051379.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051379/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051379 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=NC=NN32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 30, 90, 98, 201, 201, 201, 201, 201, 7, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 90, 90, 201, 30, 7, 7, 3, 6, 6, 6, 6, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 502
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051379 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=NC=NN32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [55, 32, 13, 1, 1, 1, 1, 1, 1, 1, 55, 55, 143, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 32, 32, 1, 55, 143, 143, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 765
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051379 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=NC=NN32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [52, 52, 52, 133, 139, 201, 201, 201, 201, 201, 12, 6, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 133, 133, 201, 52, 12, 12, 4, 1, 1, 1, 1, 6, 6, 6, 6] 201
rigid atoms, others: [34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 609
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051379 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051379
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051379/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051379
Building REAL300025051380
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051380'
/scratch/stefan/7786831/working/building/REAL300025051380 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051380

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051380/0 /scratch/stefan/7786831/working/building/REAL300025051380 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 242)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/242
`/scratch/stefan/7786831/working/3D/242' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=NC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051380.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051380.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051380/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051380 none CN1C=NC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 6, 25, 25, 25, 92, 119, 186, 186, 186, 186, 186, 1, 1, 4, 4, 4, 4, 4, 2, 6, 6, 25, 92, 92, 186, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 492
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051380 none CN1C=NC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 12, 58, 58, 58, 139, 161, 201, 201, 201, 201, 201, 4, 4, 2, 2, 2, 1, 1, 4, 12, 12, 58, 139, 139, 201, 4, 4, 4, 4] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 625
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051380 none CN1C=NC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 186, 186, 186, 186, 157, 76, 76, 34, 76, 13, 1, 1, 1, 1, 1, 1, 1, 186, 186, 201, 201, 201, 201, 201, 186, 157, 157, 76, 34, 34, 1, 186, 186, 186, 186] 201
rigid atoms, others: [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, 33, 34, 36, 37, 38, 39])
total number of confs: 724
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051380 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051380
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051380/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051380
Building REAL300025051381
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051381'
/scratch/stefan/7786831/working/building/REAL300025051381 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051381

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051381/0 /scratch/stefan/7786831/working/building/REAL300025051381 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 243)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/243
`/scratch/stefan/7786831/working/3D/243' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=CC=CN=C32)CC1)

`REAL300025051381.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051381.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051381/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051381 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=CC=CN=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 26, 76, 83, 169, 169, 169, 169, 169, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 76, 76, 169, 26, 6, 6, 3, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 42, 11, 12, 13, 44, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 434
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051381 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=CC=CN=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 31, 13, 1, 1, 1, 1, 1, 1, 1, 60, 60, 127, 169, 169, 169, 169, 201, 201, 201, 201, 201, 201, 201, 201, 201, 169, 169, 31, 31, 1, 60, 127, 127, 169, 201, 201, 201, 201, 201, 201, 169, 169, 169, 169] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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])
total number of confs: 697
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051381 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=CC=CN=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [50, 50, 50, 127, 135, 201, 201, 201, 201, 201, 13, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 127, 127, 201, 50, 13, 13, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [35, 36, 37, 38, 39, 40, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44])
total number of confs: 637
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051381 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051381
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051381/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051381
Building REAL300025051382
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051382'
/scratch/stefan/7786831/working/building/REAL300025051382 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051382

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051382/0 /scratch/stefan/7786831/working/building/REAL300025051382 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 244)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/244
`/scratch/stefan/7786831/working/3D/244' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CC=C(F)C=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051382.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051382.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051382/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051382 none O=C(CCC1=CC=C(F)C=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 9, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 7, 15, 15, 15, 40, 56, 141, 141, 141, 141, 141, 1, 1, 9, 9, 11, 11, 11, 11, 11, 11, 2, 7, 7, 15, 40, 40, 141, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 348
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051382 none O=C(CCC1=CC=C(F)C=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 11, 11, 34, 45, 45, 45, 105, 130, 201, 201, 201, 201, 201, 11, 11, 3, 3, 1, 1, 1, 1, 1, 1, 11, 34, 34, 45, 105, 105, 201, 11, 11, 11, 11] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 29, 30, 31] set([0, 1, 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, 43, 44, 45])
total number of confs: 615
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051382 none O=C(CCC1=CC=C(F)C=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [141, 141, 141, 201, 201, 201, 201, 201, 201, 201, 201, 141, 110, 59, 59, 30, 59, 13, 1, 1, 1, 1, 1, 1, 1, 141, 141, 201, 201, 201, 201, 201, 201, 201, 201, 141, 110, 110, 59, 30, 30, 1, 141, 141, 141, 141] 201
rigid atoms, others: [41, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 867
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051382 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051382
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051382/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051382
Building REAL300025051383
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051383'
/scratch/stefan/7786831/working/building/REAL300025051383 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051383

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051383/0 /scratch/stefan/7786831/working/building/REAL300025051383 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 245)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/245
`/scratch/stefan/7786831/working/3D/245' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CC=CN=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051383.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051383.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051383/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051383 none O=C(CCC1=CC=CN=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 9, 11, 19, 19, 19, 19, 19, 1, 1, 1, 6, 14, 14, 14, 43, 67, 138, 138, 138, 138, 138, 1, 1, 9, 9, 11, 11, 19, 19, 19, 19, 2, 6, 6, 14, 43, 43, 138, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 10, 11, 12, 44, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 377
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051383 none O=C(CCC1=CC=CN=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 7, 3, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 34, 49, 49, 49, 98, 132, 201, 201, 201, 201, 201, 19, 19, 7, 7, 3, 3, 1, 1, 1, 1, 19, 34, 34, 49, 98, 98, 201, 19, 19, 19, 19] 201
rigid atoms, others: [32, 33, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 621
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051383 none O=C(CCC1=CC=CN=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [138, 138, 138, 187, 188, 201, 201, 201, 201, 201, 138, 121, 66, 66, 31, 66, 13, 1, 1, 1, 1, 1, 1, 1, 138, 138, 187, 187, 188, 188, 201, 201, 201, 201, 138, 121, 121, 66, 31, 31, 1, 138, 138, 138, 138] 201
rigid atoms, others: [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, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 781
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051383 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051383
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051383/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051383
Building REAL300025051384
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051384'
/scratch/stefan/7786831/working/building/REAL300025051384 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051384

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051384/0 /scratch/stefan/7786831/working/building/REAL300025051384 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 246)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/246
`/scratch/stefan/7786831/working/3D/246' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(F)=C1)

`REAL300025051384.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051384.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051384/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051384 none COC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 4, 2, 4, 4, 2, 2, 2, 1, 1, 1, 7, 22, 22, 22, 60, 67, 174, 174, 174, 174, 174, 1, 1, 4, 4, 4, 7, 7, 7, 4, 4, 2, 7, 7, 22, 60, 60, 174, 1, 1, 1, 1, 4] 201
rigid atoms, others: [39, 8, 9, 10, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 43])
total number of confs: 424
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051384 none COC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 4, 4, 15, 38, 38, 38, 89, 98, 201, 201, 201, 201, 201, 4, 4, 1, 1, 1, 3, 3, 3, 1, 1, 4, 15, 15, 38, 89, 89, 201, 4, 4, 4, 4, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 43, 24, 25, 26, 30, 31] set([0, 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])
total number of confs: 541
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051384 none COC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 176, 201, 201, 174, 174, 174, 174, 104, 41, 41, 25, 41, 12, 1, 1, 1, 1, 1, 1, 1, 174, 174, 201, 201, 201, 201, 201, 201, 201, 201, 174, 104, 104, 41, 25, 25, 1, 174, 174, 174, 174, 201] 201
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42, 43])
total number of confs: 802
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051384 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051384
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051384/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051384
Building REAL300025051385
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051385'
/scratch/stefan/7786831/working/building/REAL300025051385 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051385

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051385/0 /scratch/stefan/7786831/working/building/REAL300025051385 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 247)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/247
`/scratch/stefan/7786831/working/3D/247' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CNC3=CC=CC=C23)CC1)

`REAL300025051385.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051385.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051385/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051385 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CNC3=CC=CC=C23)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 74, 92, 175, 175, 175, 175, 175, 6, 1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 74, 74, 175, 22, 6, 6, 3, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
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: REAL300025051385 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CNC3=CC=CC=C23)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 34, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 145, 175, 175, 175, 175, 201, 201, 201, 201, 201, 201, 201, 201, 175, 175, 34, 34, 1, 78, 145, 145, 175, 201, 201, 201, 201, 201, 201, 175, 175, 175, 175] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 703
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051385 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CNC3=CC=CC=C23)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 61, 61, 144, 156, 201, 201, 201, 201, 201, 20, 12, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 144, 144, 201, 61, 20, 20, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43])
total number of confs: 659
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051385 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051385
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051385/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051385
Building REAL300025051386
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051386'
/scratch/stefan/7786831/working/building/REAL300025051386 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051386

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051386/0 /scratch/stefan/7786831/working/building/REAL300025051386 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 248)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/248
`/scratch/stefan/7786831/working/3D/248' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C=CC(=O)NC2=O)CC1)

`REAL300025051386.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051386.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051386/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051386 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C=CC(=O)NC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 11, 8, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 61, 73, 160, 160, 160, 160, 160, 6, 1, 1, 1, 3, 3, 3, 17, 18, 18, 18, 18, 18, 18, 18, 1, 1, 61, 61, 160, 22, 6, 6, 3, 17, 17, 18, 18, 18, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
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: REAL300025051386 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C=CC(=O)NC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 11, 8, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 33, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 132, 160, 160, 160, 160, 201, 201, 201, 201, 201, 201, 201, 201, 160, 160, 33, 33, 1, 69, 132, 132, 160, 201, 201, 201, 201, 201, 160, 160, 160, 160] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 822
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051386 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C=CC(=O)NC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 11, 8, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 121, 127, 201, 201, 201, 201, 201, 28, 18, 14, 13, 2, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 121, 121, 201, 73, 28, 28, 14, 2, 2, 1, 1, 1, 18, 18, 18, 18] 201
rigid atoms, others: [36, 37, 38, 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, 39, 40, 41, 42])
total number of confs: 611
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051386 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051386
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051386/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051386
Building REAL300025051387
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051387'
/scratch/stefan/7786831/working/building/REAL300025051387 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051387

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051387/0 /scratch/stefan/7786831/working/building/REAL300025051387 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 249)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/249
`/scratch/stefan/7786831/working/3D/249' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051387.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051387.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051387/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051387 none COCC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
135  conformations in input
total number of sets (complete confs): 135
using faster count positions algorithm for large data
unique positions, atoms: [33, 21, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 5, 6, 6, 6, 9, 14, 50, 50, 50, 50, 50, 1, 1, 5, 33, 33, 33, 21, 21, 5, 5, 5, 2, 5, 5, 6, 9, 9, 50, 1, 1, 1, 1, 5] 135
rigid atoms, others: [43, 44, 10, 11, 12, 45, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46])
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: REAL300025051387 none COCC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
135  conformations in input
total number of sets (complete confs): 135
using faster count positions algorithm for large data
unique positions, atoms: [16, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 11, 11, 11, 17, 27, 89, 89, 89, 89, 89, 5, 5, 1, 16, 16, 16, 8, 8, 1, 1, 1, 5, 10, 10, 11, 17, 17, 89, 5, 5, 5, 5, 1] 135
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 46, 26] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 214
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051387 none COCC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
135  conformations in input
total number of sets (complete confs): 135
using faster count positions algorithm for large data
unique positions, atoms: [135, 135, 89, 89, 89, 89, 89, 50, 50, 50, 50, 42, 41, 41, 29, 41, 13, 1, 1, 1, 1, 1, 1, 1, 50, 50, 89, 135, 135, 135, 135, 135, 89, 89, 89, 50, 42, 42, 41, 29, 29, 1, 50, 50, 50, 50, 89] 135
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46])
total number of confs: 474
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051387 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051387
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051387/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051387
Building REAL300025051388
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051388'
/scratch/stefan/7786831/working/building/REAL300025051388 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051388

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051388/0 /scratch/stefan/7786831/working/building/REAL300025051388 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 250)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/250
`/scratch/stefan/7786831/working/3D/250' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)S1)

`REAL300025051388.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051388.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051388/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051388 none CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 14, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 2, 2, 2, 1, 1, 1, 5, 21, 21, 21, 61, 73, 163, 163, 163, 163, 163, 1, 1, 7, 7, 7, 7, 7, 7, 7, 2, 5, 5, 21, 61, 61, 163, 1, 1, 1, 1, 7, 7, 7] 201
rigid atoms, others: [36, 37, 6, 7, 8, 39, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 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, 40, 41, 42])
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: REAL300025051388 none CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 14, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 7, 17, 58, 58, 58, 127, 140, 200, 201, 201, 201, 201, 7, 7, 1, 1, 1, 2, 2, 2, 1, 7, 17, 17, 58, 127, 127, 201, 7, 7, 7, 7, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 22, 23, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 634
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051388 none CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 14, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 163, 163, 163, 163, 111, 54, 54, 26, 54, 12, 1, 1, 1, 1, 1, 1, 1, 163, 163, 201, 201, 201, 201, 201, 201, 201, 163, 111, 111, 54, 26, 26, 1, 163, 163, 163, 163, 201, 201, 201] 201
rigid atoms, others: [35, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 691
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051388 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051388
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051388/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051388
Building REAL300025051389
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051389'
/scratch/stefan/7786831/working/building/REAL300025051389 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051389

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051389/0 /scratch/stefan/7786831/working/building/REAL300025051389 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 251)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/251
`/scratch/stefan/7786831/working/3D/251' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)NCCCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051389.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051389.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051389/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051389 none NC(=O)NCCCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 74, 72, 73, 43, 43, 43, 43, 38, 38, 38, 23, 38, 13, 1, 1, 1, 1, 1, 1, 1, 43, 43, 79, 79, 79, 79, 79, 74, 74, 74, 74, 73, 73, 43, 38, 38, 38, 23, 23, 1, 43, 43, 43, 43] 79
rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 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: REAL300025051389 none NC(=O)NCCCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
79  conformations in input
total number of sets (complete confs): 79
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 11, 9, 8, 6, 2, 2, 2, 1, 1, 1, 3, 4, 4, 4, 10, 17, 43, 43, 43, 43, 43, 1, 1, 11, 11, 11, 11, 11, 9, 9, 9, 9, 6, 6, 2, 3, 3, 4, 10, 10, 43, 1, 1, 1, 1] 79
rigid atoms, others: [44, 10, 11, 12, 45, 46, 47, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 142
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051389 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051389
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051389/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051389
Building REAL300025051390
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051390'
/scratch/stefan/7786831/working/building/REAL300025051390 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051390

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051390/0 /scratch/stefan/7786831/working/building/REAL300025051390 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 252)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/252
`/scratch/stefan/7786831/working/3D/252' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1)

`REAL300025051390.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051390.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051390/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051390 none CCC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 7, 17, 17, 17, 52, 59, 117, 117, 117, 117, 117, 1, 1, 3, 5, 5, 5, 5, 5, 3, 3, 2, 7, 7, 17, 52, 52, 117, 1, 1, 1, 1] 201
rigid atoms, others: [39, 8, 9, 10, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 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: REAL300025051390 none CCC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 9, 20, 20, 20, 54, 61, 117, 117, 117, 117, 117, 3, 3, 1, 3, 3, 3, 3, 3, 1, 1, 3, 9, 9, 20, 54, 54, 117, 3, 3, 3, 3] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 24, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 330
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051390 none CCC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 117, 117, 117, 117, 117, 117, 117, 117, 82, 46, 46, 30, 46, 13, 1, 1, 1, 1, 1, 1, 1, 117, 117, 117, 201, 201, 201, 201, 201, 117, 117, 117, 82, 82, 46, 30, 30, 1, 117, 117, 117, 117] 201
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42])
total number of confs: 960
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051390 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051390
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051390/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051390
Building REAL300025051391
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051391'
/scratch/stefan/7786831/working/building/REAL300025051391 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051391

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051391/0 /scratch/stefan/7786831/working/building/REAL300025051391 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 253)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/253
`/scratch/stefan/7786831/working/3D/253' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C(C)=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1C)

`REAL300025051391.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051391.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051391/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051391 none CCN1C(C)=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', '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, 8, 1, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 6, 6, 6, 6, 6, 2, 2, 2, 1, 1, 1, 6, 12, 12, 12, 31, 42, 87, 87, 87, 87, 87, 1, 1, 6, 6, 10, 10, 10, 10, 10, 6, 6, 6, 6, 2, 6, 6, 12, 31, 31, 87, 1, 1, 1, 1, 6, 6, 6] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 46, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49])
total number of confs: 243
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051391 none CCN1C(C)=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', '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, 8, 1, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 14, 20, 20, 20, 51, 62, 113, 113, 113, 113, 113, 6, 6, 1, 1, 3, 3, 3, 2, 2, 2, 2, 2, 1, 6, 14, 14, 20, 51, 51, 113, 6, 6, 6, 6, 2, 2, 2] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 35, 25, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 322
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051391 none CCN1C(C)=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', '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, 8, 1, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 113, 113, 113, 113, 113, 87, 87, 87, 87, 68, 42, 42, 23, 42, 13, 1, 1, 1, 1, 1, 1, 1, 87, 87, 113, 113, 201, 201, 201, 201, 201, 113, 113, 113, 113, 87, 68, 68, 42, 23, 23, 1, 87, 87, 87, 87, 113, 113, 113] 201
rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 931
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051391 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051391
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051391/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051391
Building REAL300025051392
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051392'
/scratch/stefan/7786831/working/building/REAL300025051392 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051392

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051392/0 /scratch/stefan/7786831/working/building/REAL300025051392 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 254)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/254
`/scratch/stefan/7786831/working/3D/254' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1)

`REAL300025051392.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051392.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051392/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051392 none CC1=CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 7, 7, 5, 2, 2, 2, 1, 1, 1, 6, 22, 22, 22, 61, 72, 155, 155, 155, 155, 155, 1, 1, 7, 7, 7, 7, 7, 7, 7, 5, 5, 2, 6, 6, 22, 61, 61, 155, 1, 1, 1, 1, 7, 7] 201
rigid atoms, others: [8, 9, 10, 43, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 44, 45])
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: REAL300025051392 none CC1=CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 23, 43, 43, 43, 101, 125, 201, 201, 201, 201, 201, 8, 8, 1, 1, 2, 2, 2, 1, 1, 5, 5, 8, 23, 23, 43, 101, 101, 201, 8, 8, 8, 8, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 45, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 594
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051392 none CC1=CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 155, 155, 155, 155, 118, 54, 54, 28, 54, 13, 1, 1, 1, 1, 1, 1, 1, 155, 155, 201, 201, 201, 201, 201, 201, 201, 201, 201, 155, 118, 118, 54, 28, 28, 1, 155, 155, 155, 155, 201, 201] 201
rigid atoms, others: [39, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45])
total number of confs: 818
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051392 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051392
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051392/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051392
Building REAL300025051393
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051393'
/scratch/stefan/7786831/working/building/REAL300025051393 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051393

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051393/0 /scratch/stefan/7786831/working/building/REAL300025051393 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 255)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/255
`/scratch/stefan/7786831/working/3D/255' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)SN=N1)

`REAL300025051393.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051393.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051393/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051393 none CCC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)SN=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 4, 4, 2, 2, 2, 1, 1, 1, 7, 15, 15, 15, 48, 65, 158, 158, 158, 158, 158, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 2, 7, 7, 15, 48, 48, 158, 1, 1, 1, 1] 201
rigid atoms, others: [37, 6, 7, 8, 39, 40, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 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, 36])
total number of confs: 382
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051393 none CCC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)SN=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 3, 3, 4, 4, 11, 19, 19, 19, 55, 72, 160, 160, 160, 160, 160, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 11, 11, 19, 55, 55, 160, 4, 4, 4, 4] 201
rigid atoms, others: [1, 2, 3, 4, 22, 23, 24] set([0, 5, 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, 36, 37, 38, 39, 40])
total number of confs: 397
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051393 none CCC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)SN=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 160, 160, 158, 158, 158, 158, 110, 55, 55, 26, 55, 12, 1, 1, 1, 1, 1, 1, 1, 158, 158, 160, 160, 160, 201, 201, 201, 201, 201, 158, 110, 110, 55, 26, 26, 1, 158, 158, 158, 158] 201
rigid atoms, others: [36, 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, 37, 38, 39, 40])
total number of confs: 847
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051393 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051393
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051393/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051393
Building REAL300025051394
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051394'
/scratch/stefan/7786831/working/building/REAL300025051394 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051394

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051394/0 /scratch/stefan/7786831/working/building/REAL300025051394 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 256)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/256
`/scratch/stefan/7786831/working/3D/256' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCN1C(=O)CCC1=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051394.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051394.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051394/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051394 none O=C(CCN1C(=O)CCC1=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 10, 13, 15, 15, 15, 15, 15, 15, 1, 1, 1, 6, 10, 10, 10, 40, 66, 159, 159, 159, 159, 159, 1, 1, 10, 10, 13, 13, 15, 15, 15, 15, 2, 6, 6, 10, 40, 40, 159, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 394
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051394 none O=C(CCN1C(=O)CCC1=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 6, 5, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 35, 53, 53, 53, 109, 143, 201, 201, 201, 201, 201, 20, 20, 6, 6, 5, 5, 1, 1, 1, 1, 20, 35, 35, 53, 109, 109, 201, 20, 20, 20, 20] 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, 43, 44, 45])
total number of confs: 634
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051394 none O=C(CCN1C(=O)CCC1=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [159, 159, 159, 200, 201, 201, 201, 201, 201, 201, 201, 159, 135, 71, 71, 28, 71, 13, 1, 1, 1, 1, 1, 1, 1, 159, 159, 200, 200, 201, 201, 201, 201, 201, 201, 159, 135, 135, 71, 28, 28, 1, 159, 159, 159, 159] 201
rigid atoms, others: [41, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 839
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051394 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051394
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051394/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051394
Building REAL300025051395
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051395'
/scratch/stefan/7786831/working/building/REAL300025051395 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051395

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051395/0 /scratch/stefan/7786831/working/building/REAL300025051395 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 257)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/257
`/scratch/stefan/7786831/working/3D/257' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCS(=O)(=O)C2)CC1)

`REAL300025051395.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051395.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051395/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051395 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCS(=O)(=O)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 14, 11, 11, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
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, 69, 86, 158, 158, 158, 158, 158, 5, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 1, 1, 69, 69, 158, 23, 5, 5, 3, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 428
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051395 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCS(=O)(=O)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 14, 11, 11, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [77, 35, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 127, 158, 158, 158, 158, 201, 201, 201, 201, 201, 201, 158, 158, 35, 35, 1, 77, 127, 127, 158, 201, 201, 201, 201, 201, 201, 201, 158, 158, 158, 158] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 748
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051395 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCS(=O)(=O)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 14, 11, 11, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
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, 146, 162, 201, 201, 201, 201, 201, 25, 15, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 15, 15, 146, 146, 201, 76, 25, 25, 9, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42])
total number of confs: 671
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051395 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051395
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051395/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051395
Building REAL300025051396
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051396'
/scratch/stefan/7786831/working/building/REAL300025051396 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051396

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051396/0 /scratch/stefan/7786831/working/building/REAL300025051396 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 258)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/258
`/scratch/stefan/7786831/working/3D/258' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1CCCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025051396.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051396.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051396/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051396 none CC(=O)N1CCCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 9, 13, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 7, 12, 12, 12, 36, 50, 130, 130, 130, 130, 130, 1, 1, 9, 13, 13, 13, 9, 9, 9, 9, 9, 9, 9, 2, 7, 7, 12, 36, 36, 130, 1, 1, 1, 1, 9, 9] 201
rigid atoms, others: [44, 10, 11, 12, 45, 46, 47, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49])
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: REAL300025051396 none CC(=O)N1CCCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 21, 32, 32, 32, 74, 94, 187, 187, 187, 187, 187, 9, 9, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 9, 21, 21, 32, 74, 74, 187, 9, 9, 9, 9, 1, 1] 201
rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 8, 7, 48, 49, 35, 36, 26, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 503
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051396 none CC(=O)N1CCCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 187, 201, 187, 187, 187, 187, 130, 130, 130, 130, 105, 58, 58, 28, 58, 13, 1, 1, 1, 1, 1, 1, 1, 130, 130, 187, 201, 201, 201, 187, 187, 187, 187, 187, 187, 187, 130, 105, 105, 58, 28, 28, 1, 130, 130, 130, 130, 187, 187] 201
rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49])
total number of confs: 740
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051396 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051396
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051396/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051396
Building REAL300025051397
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051397'
/scratch/stefan/7786831/working/building/REAL300025051397 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051397

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051397/0 /scratch/stefan/7786831/working/building/REAL300025051397 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 259)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/259
`/scratch/stefan/7786831/working/3D/259' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3=CC=CC=C3O2)CC1)

`REAL300025051397.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051397.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051397/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051397 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3=CC=CC=C3O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 25, 71, 74, 173, 173, 173, 173, 173, 6, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 71, 71, 173, 25, 6, 6, 3, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 42, 11, 12, 13, 44, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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])
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: REAL300025051397 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3=CC=CC=C3O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 13, 1, 1, 1, 1, 1, 1, 1, 58, 58, 125, 173, 173, 173, 173, 201, 201, 201, 201, 201, 201, 201, 201, 173, 173, 32, 32, 1, 58, 125, 125, 173, 201, 201, 201, 201, 201, 201, 201, 173, 173, 173, 173] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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: 760
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051397 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3=CC=CC=C3O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 61, 61, 132, 135, 201, 201, 201, 201, 201, 18, 10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 132, 132, 201, 61, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44])
total number of confs: 643
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051397 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051397
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051397/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051397
Building REAL300025051398
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051398'
/scratch/stefan/7786831/working/building/REAL300025051398 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051398

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051398/0 /scratch/stefan/7786831/working/building/REAL300025051398 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 260)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/260
`/scratch/stefan/7786831/working/3D/260' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(Cl)C=C2F)CC1)

`REAL300025051398.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051398.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051398/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051398 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(Cl)C=C2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 29, 93, 103, 189, 189, 189, 189, 189, 7, 1, 1, 1, 3, 3, 3, 10, 10, 4, 10, 10, 10, 10, 1, 1, 93, 93, 189, 29, 7, 7, 3, 10, 10, 10, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 519
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051398 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(Cl)C=C2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [68, 33, 13, 1, 1, 1, 1, 1, 1, 1, 68, 68, 140, 189, 189, 189, 189, 201, 201, 190, 201, 201, 201, 201, 189, 189, 33, 33, 1, 68, 140, 140, 189, 201, 201, 201, 189, 189, 189, 189] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 777
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051398 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(Cl)C=C2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 143, 151, 201, 201, 201, 201, 201, 19, 10, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 143, 143, 201, 60, 19, 19, 7, 1, 1, 1, 10, 10, 10, 10] 201
rigid atoms, others: [33, 34, 35, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39])
total number of confs: 663
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051398 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051398
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051398/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051398
Building REAL300025051399
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051399'
/scratch/stefan/7786831/working/building/REAL300025051399 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051399

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051399/0 /scratch/stefan/7786831/working/building/REAL300025051399 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 261)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/261
`/scratch/stefan/7786831/working/3D/261' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(C3CC3)=NO2)CC1)

`REAL300025051399.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051399.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051399/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051399 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(C3CC3)=NO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 41, 47, 102, 102, 102, 102, 102, 5, 1, 1, 1, 3, 3, 3, 14, 14, 14, 63, 63, 14, 14, 1, 1, 41, 41, 102, 16, 5, 5, 3, 14, 63, 63, 63, 63, 63, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
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: REAL300025051399 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(C3CC3)=NO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [52, 28, 13, 1, 1, 1, 1, 1, 1, 1, 52, 52, 83, 102, 102, 102, 102, 130, 130, 130, 201, 201, 130, 130, 102, 102, 28, 28, 1, 52, 83, 83, 102, 130, 201, 201, 201, 201, 201, 102, 102, 102, 102] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 714
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051399 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(C3CC3)=NO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 138, 138, 185, 187, 201, 201, 201, 201, 201, 79, 63, 46, 46, 12, 46, 12, 12, 1, 1, 1, 1, 12, 12, 63, 63, 185, 185, 201, 138, 79, 79, 46, 12, 1, 1, 1, 1, 1, 63, 63, 63, 63] 201
rigid atoms, others: [34, 35, 36, 37, 38, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42])
total number of confs: 748
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051399 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(C3CC3)=NO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 90, 92, 130, 130, 130, 130, 130, 21, 14, 10, 10, 1, 10, 1, 1, 1, 1, 12, 12, 1, 1, 14, 14, 90, 90, 130, 52, 21, 21, 10, 1, 12, 12, 12, 12, 12, 14, 14, 14, 14] 201
rigid atoms, others: [33, 14, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 457
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051399 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051399
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051399/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051399
Building REAL300025051400
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051400'
/scratch/stefan/7786831/working/building/REAL300025051400 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051400

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051400/0 /scratch/stefan/7786831/working/building/REAL300025051400 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 262)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/262
`/scratch/stefan/7786831/working/3D/262' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=NO1)

`REAL300025051400.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051400.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051400/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051400 none CCC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 6, 6, 2, 2, 2, 1, 1, 1, 4, 11, 11, 11, 35, 53, 161, 161, 161, 161, 161, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 2, 4, 4, 11, 35, 35, 161, 1, 1, 1, 1, 6] 201
rigid atoms, others: [37, 6, 7, 8, 39, 40, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 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, 36, 41])
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: REAL300025051400 none CCC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 1, 1, 1, 6, 6, 6, 6, 12, 24, 24, 24, 65, 90, 182, 182, 182, 182, 182, 6, 6, 1, 1, 1, 5, 5, 5, 5, 5, 6, 12, 12, 24, 65, 65, 182, 6, 6, 6, 6, 1] 201
rigid atoms, others: [1, 2, 3, 4, 41, 22, 23, 24] set([0, 5, 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, 36, 37, 38, 39, 40])
total number of confs: 465
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051400 none CCC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 182, 182, 161, 161, 161, 161, 129, 65, 65, 25, 65, 12, 1, 1, 1, 1, 1, 1, 1, 161, 161, 182, 182, 182, 201, 201, 201, 201, 201, 161, 129, 129, 65, 25, 25, 1, 161, 161, 161, 161, 182] 201
rigid atoms, others: [36, 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, 37, 38, 39, 40, 41])
total number of confs: 776
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051400 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051400
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051400/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051400
Building REAL300025051401
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051401'
/scratch/stefan/7786831/working/building/REAL300025051401 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051401

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051401/0 /scratch/stefan/7786831/working/building/REAL300025051401 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 263)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/263
`/scratch/stefan/7786831/working/3D/263' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1=CC=CS1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051401.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051401.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051401/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051401 none CC(CC1=CC=CS1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 14, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 2, 6, 13, 17, 17, 17, 17, 2, 2, 1, 1, 1, 4, 8, 8, 8, 25, 39, 89, 89, 89, 89, 89, 1, 1, 6, 6, 6, 6, 13, 13, 17, 17, 17, 2, 4, 4, 8, 25, 25, 89, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
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: REAL300025051401 none CC(CC1=CC=CS1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 14, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 3, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 17, 33, 52, 52, 52, 93, 122, 201, 201, 201, 201, 201, 17, 17, 7, 7, 7, 7, 3, 3, 1, 1, 1, 17, 33, 33, 52, 93, 93, 201, 17, 17, 17, 17] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 602
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051401 none CC(CC1=CC=CS1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 14, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [147, 89, 147, 170, 201, 201, 201, 201, 89, 89, 89, 79, 50, 50, 24, 50, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 147, 147, 147, 147, 170, 170, 201, 201, 201, 89, 79, 79, 50, 24, 24, 1, 89, 89, 89, 89] 201
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 808
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051401 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051401
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051401/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051401
Building REAL300025051402
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051402'
/scratch/stefan/7786831/working/building/REAL300025051402 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051402

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051402/0 /scratch/stefan/7786831/working/building/REAL300025051402 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 264)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/264
`/scratch/stefan/7786831/working/3D/264' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C1=NC=CN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051402.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051402.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051402/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051402 none CC(C)C1=NC=CN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 13, 26, 13, 13, 13, 13, 7, 2, 2, 2, 1, 1, 1, 3, 5, 5, 5, 15, 23, 71, 71, 71, 71, 71, 1, 1, 26, 26, 26, 26, 26, 26, 26, 13, 13, 7, 7, 2, 3, 3, 5, 15, 15, 71, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 46, 45, 48, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
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: REAL300025051402 none CC(C)C1=NC=CN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 13, 13, 13, 13, 21, 33, 33, 33, 85, 120, 201, 201, 201, 201, 201, 13, 13, 4, 4, 4, 3, 4, 4, 4, 1, 1, 4, 4, 13, 21, 21, 33, 85, 85, 201, 13, 13, 13, 13] 201
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 35] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 602
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051402 none CC(C)C1=NC=CN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 166, 71, 71, 71, 71, 59, 42, 42, 25, 42, 12, 1, 1, 1, 1, 1, 1, 1, 71, 71, 201, 201, 201, 201, 201, 201, 201, 201, 201, 166, 166, 71, 59, 59, 42, 25, 25, 1, 71, 71, 71, 71] 201
rigid atoms, others: [44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48])
total number of confs: 763
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051402 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051402/1 /scratch/stefan/7786831/working/building/REAL300025051402 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 265)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/265
`/scratch/stefan/7786831/working/3D/265' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C1=[NH+]C=CN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051402.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051402.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051402/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051402 none CC(C)C1=[NH+]C=CN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 6, 1, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [7, 4, 7, 4, 4, 4, 4, 4, 3, 2, 2, 2, 1, 1, 1, 2, 3, 3, 3, 6, 7, 8, 8, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 4, 4, 3, 3, 2, 2, 2, 3, 6, 6, 8, 1, 1, 1, 1] 14
rigid atoms, others: [12, 13, 46, 47, 48, 49, 14, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
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: REAL300025051402 none CC(C)C1=[NH+]C=CN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 6, 1, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 7, 7, 7, 11, 12, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 3, 3, 4, 4, 4, 7, 11, 11, 14, 4, 4, 4, 4] 14
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 35, 36] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 68
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051402 none CC(C)C1=[NH+]C=CN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 6, 1, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 10, 8, 8, 8, 8, 8, 8, 8, 6, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 10, 10, 8, 8, 8, 8, 6, 6, 1, 8, 8, 8, 8] 14
rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49])
total number of confs: 40
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051402 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051402
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051402/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051402/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051402
Building REAL300025051403
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051403'
/scratch/stefan/7786831/working/building/REAL300025051403 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051403

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051403/0 /scratch/stefan/7786831/working/building/REAL300025051403 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 266)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/266
`/scratch/stefan/7786831/working/3D/266' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C(C3CC3)N=C2)CC1)

`REAL300025051403.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051403.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051403/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051403 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C(C3CC3)N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 26, 31, 116, 116, 116, 116, 116, 4, 1, 1, 1, 3, 3, 3, 7, 7, 3, 3, 21, 21, 7, 7, 1, 1, 26, 26, 116, 10, 4, 4, 3, 7, 21, 21, 21, 21, 21, 7, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 42, 11, 12, 13, 44, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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])
total number of confs: 283
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051403 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C(C3CC3)N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 39, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 100, 116, 116, 116, 116, 143, 143, 116, 116, 201, 201, 143, 143, 116, 116, 39, 39, 1, 75, 100, 100, 116, 143, 201, 201, 201, 201, 201, 143, 116, 116, 116, 116] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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: 897
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051403 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C(C3CC3)N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [51, 51, 51, 108, 115, 201, 201, 201, 201, 201, 30, 21, 16, 16, 1, 16, 1, 11, 11, 1, 1, 1, 1, 11, 11, 21, 21, 108, 108, 201, 51, 30, 30, 16, 12, 1, 1, 1, 1, 1, 12, 21, 21, 21, 21] 201
rigid atoms, others: [35, 36, 37, 38, 39, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44])
total number of confs: 620
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051403 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C(C3CC3)N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 57, 64, 143, 143, 143, 143, 143, 10, 7, 5, 5, 1, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 57, 57, 143, 24, 10, 10, 5, 1, 11, 12, 11, 11, 12, 1, 7, 7, 7, 7] 201
rigid atoms, others: [34, 40, 14, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 389
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051403 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051403
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051403/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051403
Building REAL300025051404
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051404'
/scratch/stefan/7786831/working/building/REAL300025051404 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051404

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051404/0 /scratch/stefan/7786831/working/building/REAL300025051404 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 267)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/267
`/scratch/stefan/7786831/working/3D/267' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CSC=N2)CC1)

`REAL300025051404.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051404.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051404/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051404 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CSC=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 18, 43, 52, 142, 142, 142, 142, 142, 5, 1, 1, 1, 3, 3, 3, 20, 28, 28, 28, 28, 1, 1, 43, 43, 142, 18, 5, 5, 3, 20, 20, 28, 28, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 379
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051404 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CSC=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [58, 29, 13, 1, 1, 1, 1, 1, 1, 1, 58, 58, 104, 142, 142, 142, 142, 198, 201, 201, 201, 201, 142, 142, 29, 29, 1, 58, 104, 104, 142, 198, 198, 201, 201, 142, 142, 142, 142] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 829
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051404 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CSC=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [89, 89, 89, 142, 147, 201, 201, 201, 201, 201, 40, 28, 20, 20, 3, 20, 1, 1, 1, 1, 1, 1, 28, 28, 142, 142, 201, 89, 40, 40, 20, 3, 3, 1, 1, 28, 28, 28, 28] 201
rigid atoms, others: [33, 34, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38])
total number of confs: 669
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051404 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051404
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051404/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051404
Building REAL300025051405
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051405'
/scratch/stefan/7786831/working/building/REAL300025051405 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051405

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051405/0 /scratch/stefan/7786831/working/building/REAL300025051405 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 268)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/268
`/scratch/stefan/7786831/working/3D/268' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCN(C(=O)C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1)

`REAL300025051405.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051405.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051405/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051405 none CC1CCN(C(=O)C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 13, 6, 2, 6, 2, 2, 1, 1, 1, 6, 15, 15, 15, 42, 63, 142, 142, 142, 142, 142, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 6, 6, 15, 42, 42, 142, 1, 1, 1, 1, 13, 13, 13, 13] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49])
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: REAL300025051405 none CC1CCN(C(=O)C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 13, 13, 13, 13, 24, 36, 36, 36, 80, 114, 201, 201, 201, 201, 201, 13, 13, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 13, 24, 24, 36, 80, 80, 201, 13, 13, 13, 13, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 46, 47, 48, 49, 25, 26, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 532
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051405 none CC1CCN(C(=O)C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 172, 142, 172, 142, 142, 142, 121, 77, 77, 31, 77, 13, 1, 1, 1, 1, 1, 1, 1, 142, 142, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 142, 121, 121, 77, 31, 31, 1, 142, 142, 142, 142, 201, 201, 201, 201] 201
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 716
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051405 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051405
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051405/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051405
Building REAL300025051406
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051406'
/scratch/stefan/7786831/working/building/REAL300025051406 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051406

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051406/0 /scratch/stefan/7786831/working/building/REAL300025051406 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 269)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/269
`/scratch/stefan/7786831/working/3D/269' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCCN(C(=O)C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025051406.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051406.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051406/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051406 none CC1CCCN(C(=O)C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 12, 12, 12, 6, 2, 6, 2, 2, 1, 1, 1, 6, 16, 16, 16, 47, 69, 150, 152, 152, 152, 152, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 6, 6, 16, 47, 47, 152, 1, 1, 1, 1, 12, 12] 201
rigid atoms, others: [44, 10, 11, 12, 45, 46, 47, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49])
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051406 none CC1CCCN(C(=O)C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 12, 12, 12, 24, 36, 36, 36, 84, 116, 201, 201, 201, 201, 201, 12, 12, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 12, 24, 24, 36, 84, 84, 201, 12, 12, 12, 12, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 48, 49, 35, 36, 26, 5, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 554
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051406 none CC1CCCN(C(=O)C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 184, 152, 184, 152, 152, 152, 123, 71, 71, 30, 71, 13, 1, 1, 1, 1, 1, 1, 1, 152, 152, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 152, 123, 123, 71, 30, 30, 1, 152, 152, 152, 152, 201, 201] 201
rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49])
total number of confs: 744
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051406 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051406
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051406/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051406
Building REAL300025051407
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051407'
/scratch/stefan/7786831/working/building/REAL300025051407 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051407

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051407/0 /scratch/stefan/7786831/working/building/REAL300025051407 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 270)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/270
`/scratch/stefan/7786831/working/3D/270' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=NC(C)=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051407.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051407.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051407/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051407 none COC1=NC(C)=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 1, 5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 1, 1, 1, 7, 25, 25, 25, 71, 75, 184, 185, 185, 185, 185, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 7, 7, 25, 71, 71, 185, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 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: REAL300025051407 none COC1=NC(C)=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 1, 5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 19, 62, 62, 62, 133, 138, 200, 201, 201, 201, 201, 6, 6, 2, 2, 2, 2, 2, 2, 1, 1, 6, 19, 19, 62, 133, 133, 201, 6, 6, 6, 6] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 33] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 639
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051407 none COC1=NC(C)=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 1, 5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 185, 185, 185, 185, 115, 43, 43, 25, 43, 12, 1, 1, 1, 1, 1, 1, 1, 185, 185, 201, 201, 201, 201, 201, 201, 201, 201, 185, 115, 115, 43, 25, 25, 1, 185, 185, 185, 185] 201
rigid atoms, others: [41, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 711
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051407 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051407
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051407/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051407
Building REAL300025051408
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051408'
/scratch/stefan/7786831/working/building/REAL300025051408 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051408

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051408/0 /scratch/stefan/7786831/working/building/REAL300025051408 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 271)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/271
`/scratch/stefan/7786831/working/3D/271' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=COC(C3CC3)=N2)CC1)

`REAL300025051408.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051408.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051408/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051408 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=COC(C3CC3)=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 12, 1, 5, 5, 5, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 35, 37, 109, 109, 109, 109, 109, 4, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 56, 56, 10, 1, 1, 35, 35, 109, 16, 4, 4, 3, 10, 56, 56, 56, 56, 56, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
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: REAL300025051408 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=COC(C3CC3)=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 12, 1, 5, 5, 5, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 27, 13, 1, 1, 1, 1, 1, 1, 1, 35, 35, 80, 109, 109, 109, 109, 137, 137, 137, 137, 201, 201, 137, 109, 109, 27, 27, 1, 35, 80, 80, 109, 137, 201, 201, 201, 201, 201, 109, 109, 109, 109] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 724
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051408 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=COC(C3CC3)=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 12, 1, 5, 5, 5, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 182, 182, 201, 201, 201, 201, 201, 70, 56, 46, 46, 13, 46, 13, 13, 13, 1, 1, 1, 1, 13, 56, 56, 182, 182, 201, 142, 70, 70, 46, 13, 1, 1, 1, 1, 1, 56, 56, 56, 56] 201
rigid atoms, others: [34, 35, 36, 37, 38, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42])
total number of confs: 722
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051408 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=COC(C3CC3)=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 12, 1, 5, 5, 5, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 65, 65, 137, 137, 137, 137, 137, 12, 10, 7, 6, 1, 6, 1, 1, 1, 1, 1, 13, 13, 1, 10, 10, 65, 65, 137, 36, 12, 12, 7, 1, 13, 13, 13, 13, 13, 10, 10, 10, 10] 201
rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 391
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051408 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051408
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051408/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051408
Building REAL300025051409
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051409'
/scratch/stefan/7786831/working/building/REAL300025051409 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051409

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051409/0 /scratch/stefan/7786831/working/building/REAL300025051409 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 272)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/272
`/scratch/stefan/7786831/working/3D/272' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@H]2C[C@@H]2C2=CC=CC=C2)CC1)

`REAL300025051409.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051409.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051409/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051409 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@H]2C[C@@H]2C2=CC=CC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 45, 52, 129, 129, 129, 129, 129, 5, 1, 1, 1, 3, 3, 3, 19, 19, 19, 19, 19, 27, 27, 19, 27, 27, 1, 1, 45, 45, 129, 13, 5, 5, 3, 19, 19, 27, 27, 19, 27, 27, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 371
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051409 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@H]2C[C@@H]2C2=CC=CC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [66, 33, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 117, 129, 129, 129, 129, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 129, 129, 33, 33, 1, 66, 117, 117, 129, 201, 201, 201, 201, 201, 201, 201, 129, 129, 129, 129] 201
rigid atoms, others: [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, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 736
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051409 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@H]2C[C@@H]2C2=CC=CC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [75, 75, 75, 144, 151, 201, 201, 201, 201, 201, 34, 27, 18, 18, 4, 18, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 27, 27, 144, 144, 201, 75, 34, 34, 18, 4, 4, 1, 1, 1, 1, 1, 27, 27, 27, 27] 201
rigid atoms, others: [38, 39, 40, 41, 42, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46])
total number of confs: 686
number of broken/clashed sets: 1
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051409 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@H]2C[C@@H]2C2=CC=CC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [64, 64, 64, 137, 144, 201, 201, 201, 201, 201, 26, 19, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 19, 19, 137, 137, 201, 64, 26, 26, 11, 1, 1, 4, 4, 1, 4, 4, 19, 19, 19, 19] 201
rigid atoms, others: [36, 37, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 688
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051409 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051409
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051409/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051409
Building REAL300025051410
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051410'
/scratch/stefan/7786831/working/building/REAL300025051410 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051410

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051410/0 /scratch/stefan/7786831/working/building/REAL300025051410 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 273)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/273
`/scratch/stefan/7786831/working/3D/273' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2C3CC4=CC=CC=C4C32)CC1)

`REAL300025051410.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051410.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051410/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051410 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2C3CC4=CC=CC=C4C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
139  conformations in input
total number of sets (complete confs): 139
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 76, 89, 130, 130, 130, 130, 130, 7, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 76, 76, 130, 24, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1] 139
rigid atoms, others: [47, 12, 11, 44, 13, 46, 45, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 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: REAL300025051410 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2C3CC4=CC=CC=C4C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
139  conformations in input
total number of sets (complete confs): 139
using faster count positions algorithm for large data
unique positions, atoms: [74, 30, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 119, 130, 130, 130, 130, 139, 139, 139, 139, 139, 139, 139, 139, 139, 130, 130, 30, 30, 1, 74, 119, 119, 130, 139, 139, 139, 139, 139, 139, 139, 139, 139, 130, 130, 130, 130] 139
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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, 46, 47])
total number of confs: 532
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051410 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2C3CC4=CC=CC=C4C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
139  conformations in input
total number of sets (complete confs): 139
using faster count positions algorithm for large data
unique positions, atoms: [34, 34, 34, 85, 98, 139, 139, 139, 139, 139, 12, 7, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 85, 85, 139, 34, 12, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 139
rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47])
total number of confs: 418
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051410 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051410
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051410/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051410
Building REAL300025051411
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051411'
/scratch/stefan/7786831/working/building/REAL300025051411 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051411

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051411/0 /scratch/stefan/7786831/working/building/REAL300025051411 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 274)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/274
`/scratch/stefan/7786831/working/3D/274' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1)

`REAL300025051411.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051411.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051411/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051411 none COCC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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: [26, 11, 3, 3, 3, 2, 2, 2, 1, 1, 1, 4, 6, 6, 6, 21, 38, 123, 123, 123, 123, 123, 1, 1, 3, 3, 26, 26, 26, 11, 11, 3, 2, 4, 4, 6, 21, 21, 123, 1, 1, 1, 1] 201
rigid atoms, others: [39, 8, 9, 10, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 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: REAL300025051411 none COCC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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: [23, 8, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 7, 7, 7, 22, 39, 124, 124, 124, 124, 124, 3, 3, 1, 1, 24, 24, 24, 8, 8, 1, 3, 5, 5, 7, 22, 22, 124, 3, 3, 3, 3] 201
rigid atoms, others: [2, 3, 4, 5, 6, 24, 25, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 288
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051411 none COCC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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, 124, 124, 124, 123, 123, 123, 123, 101, 59, 59, 26, 59, 13, 1, 1, 1, 1, 1, 1, 1, 123, 123, 124, 124, 201, 201, 201, 201, 201, 124, 123, 101, 101, 59, 26, 26, 1, 123, 123, 123, 123] 201
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42])
total number of confs: 887
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051411 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051411
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051411/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051411
Building REAL300025051412
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051412'
/scratch/stefan/7786831/working/building/REAL300025051412 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051412

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051412/0 /scratch/stefan/7786831/working/building/REAL300025051412 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 275)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/275
`/scratch/stefan/7786831/working/3D/275' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3C=CC=NN32)CC1)

`REAL300025051412.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051412.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051412/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051412 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3C=CC=NN32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 29, 91, 107, 195, 195, 195, 195, 195, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 91, 91, 195, 29, 6, 6, 3, 7, 7, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 512
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051412 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3C=CC=NN32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [70, 32, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 151, 195, 195, 195, 195, 201, 201, 201, 201, 201, 201, 201, 201, 195, 195, 32, 32, 1, 70, 151, 151, 195, 201, 201, 201, 201, 201, 195, 195, 195, 195] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 744
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051412 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3C=CC=NN32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [51, 51, 51, 128, 142, 201, 201, 201, 201, 201, 13, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 128, 128, 201, 51, 13, 13, 4, 1, 1, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42])
total number of confs: 624
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051412 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051412
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051412/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051412
Building REAL300025051413
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051413'
/scratch/stefan/7786831/working/building/REAL300025051413 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051413

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051413/0 /scratch/stefan/7786831/working/building/REAL300025051413 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 276)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/276
`/scratch/stefan/7786831/working/3D/276' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3C=CC=NN23)CC1)

`REAL300025051413.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051413.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051413/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051413 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3C=CC=NN23)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 30, 102, 123, 197, 197, 197, 197, 197, 7, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 102, 102, 197, 30, 7, 7, 3, 7, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
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: REAL300025051413 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3C=CC=NN23)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [79, 35, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 159, 197, 197, 197, 197, 201, 201, 201, 201, 201, 201, 201, 201, 197, 197, 35, 35, 1, 79, 159, 159, 197, 201, 201, 201, 201, 197, 197, 197, 197] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 724
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051413 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3C=CC=NN23)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [50, 50, 50, 136, 151, 201, 201, 201, 201, 201, 15, 7, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 136, 136, 201, 50, 15, 15, 4, 1, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 639
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051413 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051413
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051413/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051413
Building REAL300025051414
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051414'
/scratch/stefan/7786831/working/building/REAL300025051414 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051414

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051414/0 /scratch/stefan/7786831/working/building/REAL300025051414 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 277)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/277
`/scratch/stefan/7786831/working/3D/277' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C(=O)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051414.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051414.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051414/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051414 none CN(C)C(=O)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 176, 201, 125, 125, 125, 125, 104, 64, 64, 28, 64, 13, 1, 1, 1, 1, 1, 1, 1, 125, 125, 201, 201, 201, 201, 201, 201, 176, 176, 125, 104, 104, 64, 28, 28, 1, 125, 125, 125, 125] 201
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42])
total number of confs: 855
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: REAL300025051414 none CN(C)C(=O)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 19, 22, 6, 19, 2, 2, 2, 1, 1, 1, 4, 6, 6, 6, 23, 40, 125, 125, 125, 125, 125, 1, 1, 22, 22, 22, 22, 22, 22, 6, 6, 2, 4, 4, 6, 23, 23, 125, 1, 1, 1, 1] 201
rigid atoms, others: [39, 8, 9, 10, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 300
number of broken/clashed sets: 57
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051414 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051414
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051414/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051414
Building REAL300025051415
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051415'
/scratch/stefan/7786831/working/building/REAL300025051415 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051415

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051415/0 /scratch/stefan/7786831/working/building/REAL300025051415 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 278)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/278
`/scratch/stefan/7786831/working/3D/278' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(C)C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1)

`REAL300025051415.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051415.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051415/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051415 none CC1=CC=C(C(C)C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 18, 18, 9, 2, 9, 2, 2, 1, 1, 1, 4, 7, 7, 7, 23, 38, 116, 116, 116, 116, 116, 1, 1, 18, 18, 18, 18, 18, 18, 9, 9, 9, 9, 2, 4, 4, 7, 23, 23, 116, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 272
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051415 none CC1=CC=C(C(C)C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 18, 18, 18, 18, 34, 50, 50, 50, 98, 122, 201, 201, 201, 201, 201, 18, 18, 1, 2, 2, 2, 1, 1, 9, 9, 9, 9, 18, 34, 34, 50, 98, 98, 201, 18, 18, 18, 18] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 631
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051415 none CC1=CC=C(C(C)C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 197, 116, 197, 116, 116, 116, 99, 64, 64, 27, 64, 13, 1, 1, 1, 1, 1, 1, 1, 116, 116, 201, 201, 201, 201, 201, 201, 197, 197, 197, 197, 116, 99, 99, 64, 27, 27, 1, 116, 116, 116, 116] 201
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 853
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051415 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051415
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051415/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051415
Building REAL300025051416
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051416'
/scratch/stefan/7786831/working/building/REAL300025051416 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051416

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051416/0 /scratch/stefan/7786831/working/building/REAL300025051416 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 279)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/279
`/scratch/stefan/7786831/working/3D/279' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)C1=NOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051416.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051416.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051416/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051416 none CCC(C)C1=NOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 9, 3, 9, 3, 3, 3, 2, 2, 2, 1, 1, 1, 7, 21, 21, 21, 60, 66, 128, 128, 128, 128, 128, 1, 1, 3, 12, 12, 12, 12, 12, 9, 9, 9, 9, 2, 7, 7, 21, 60, 60, 128, 1, 1, 1, 1, 3] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47])
total number of confs: 393
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051416 none CCC(C)C1=NOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 3, 9, 24, 24, 24, 66, 72, 137, 137, 137, 137, 137, 3, 3, 1, 9, 9, 9, 9, 9, 6, 6, 6, 6, 3, 9, 9, 24, 66, 66, 137, 3, 3, 3, 3, 1] 201
rigid atoms, others: [2, 4, 5, 6, 7, 8, 47, 26] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 421
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051416 none CCC(C)C1=NOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 137, 201, 137, 137, 137, 128, 128, 128, 128, 82, 39, 39, 25, 39, 12, 1, 1, 1, 1, 1, 1, 1, 128, 128, 137, 201, 201, 201, 201, 201, 201, 201, 201, 201, 128, 82, 82, 39, 25, 25, 1, 128, 128, 128, 128, 137] 201
rigid atoms, others: [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, 40, 41, 43, 44, 45, 46, 47])
total number of confs: 875
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051416 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051416
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051416/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051416
Building REAL300025051417
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051417'
/scratch/stefan/7786831/working/building/REAL300025051417 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051417

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051417/0 /scratch/stefan/7786831/working/building/REAL300025051417 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 280)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/280
`/scratch/stefan/7786831/working/3D/280' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=N1)

`REAL300025051417.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051417.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051417/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051417 none C=CCN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=N1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 10, 3, 3, 3, 2, 2, 2, 1, 1, 1, 4, 9, 9, 9, 26, 40, 136, 136, 136, 136, 136, 1, 1, 3, 3, 21, 21, 21, 10, 10, 3, 2, 4, 4, 9, 26, 26, 136, 1, 1, 1, 1] 201
rigid atoms, others: [39, 8, 9, 10, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 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: REAL300025051417 none C=CCN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=N1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 8, 1, 1, 1, 1, 1, 2, 2, 3, 3, 6, 11, 11, 11, 31, 47, 148, 148, 148, 148, 148, 3, 3, 1, 1, 18, 18, 18, 8, 8, 1, 3, 6, 6, 11, 31, 31, 148, 3, 3, 3, 3] 201
rigid atoms, others: [2, 3, 4, 5, 6, 24, 25, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 349
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051417 none C=CCN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=N1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 148, 148, 148, 136, 136, 136, 136, 107, 63, 63, 27, 63, 13, 1, 1, 1, 1, 1, 1, 1, 136, 136, 148, 148, 201, 201, 201, 201, 201, 148, 136, 107, 107, 63, 27, 27, 1, 136, 136, 136, 136] 201
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42])
total number of confs: 837
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051417 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051417
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051417/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051417
Building REAL300025051418
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051418'
/scratch/stefan/7786831/working/building/REAL300025051418 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051418

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051418/0 /scratch/stefan/7786831/working/building/REAL300025051418 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 281)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/281
`/scratch/stefan/7786831/working/3D/281' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C(C3CC3)N=CS2)CC1)

`REAL300025051418.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051418.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051418/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051418 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C(C3CC3)N=CS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 1, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
143  conformations in input
total number of sets (complete confs): 143
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 24, 30, 61, 61, 61, 61, 61, 5, 1, 1, 1, 3, 3, 3, 17, 17, 36, 36, 17, 17, 17, 1, 1, 24, 24, 61, 10, 5, 5, 3, 36, 36, 36, 36, 36, 17, 1, 1, 1, 1] 143
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 236
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051418 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C(C3CC3)N=CS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 1, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
143  conformations in input
total number of sets (complete confs): 143
using faster count positions algorithm for large data
unique positions, atoms: [44, 23, 12, 1, 1, 1, 1, 1, 1, 1, 44, 44, 58, 61, 61, 61, 61, 102, 102, 143, 143, 102, 102, 102, 61, 61, 23, 23, 1, 44, 58, 58, 61, 143, 143, 143, 143, 143, 102, 61, 61, 61, 61] 143
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 469
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051418 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C(C3CC3)N=CS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 1, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
143  conformations in input
total number of sets (complete confs): 143
using faster count positions algorithm for large data
unique positions, atoms: [76, 76, 76, 113, 122, 143, 143, 143, 143, 143, 48, 36, 26, 26, 6, 26, 6, 1, 1, 1, 1, 6, 6, 6, 36, 36, 113, 113, 143, 76, 48, 48, 26, 1, 1, 1, 1, 1, 6, 36, 36, 36, 36] 143
rigid atoms, others: [33, 34, 35, 36, 37, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42])
total number of confs: 522
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051418 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C(C3CC3)N=CS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 1, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
143  conformations in input
total number of sets (complete confs): 143
using faster count positions algorithm for large data
unique positions, atoms: [43, 43, 43, 71, 78, 102, 102, 102, 102, 102, 24, 17, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 1, 1, 17, 17, 71, 71, 102, 43, 24, 24, 11, 6, 6, 6, 6, 6, 1, 17, 17, 17, 17] 143
rigid atoms, others: [38, 14, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 363
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051418 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051418
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051418/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051418
Building REAL300025051419
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051419'
/scratch/stefan/7786831/working/building/REAL300025051419 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051419

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051419/0 /scratch/stefan/7786831/working/building/REAL300025051419 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 282)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/282
`/scratch/stefan/7786831/working/3D/282' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)SC=N1)

`REAL300025051419.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051419.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051419/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051419 none COCC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)SC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 13, 6, 6, 2, 2, 2, 1, 1, 1, 4, 7, 7, 7, 24, 40, 128, 128, 128, 128, 128, 1, 1, 6, 6, 6, 25, 25, 25, 13, 13, 2, 4, 4, 7, 24, 24, 128, 1, 1, 1, 1, 6] 201
rigid atoms, others: [38, 7, 8, 9, 39, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 42])
total number of confs: 296
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051419 none COCC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)SC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 6, 6, 6, 6, 10, 18, 18, 18, 52, 77, 165, 165, 165, 165, 165, 6, 6, 1, 1, 1, 15, 15, 15, 6, 6, 6, 10, 10, 18, 52, 52, 165, 6, 6, 6, 6, 1] 201
rigid atoms, others: [2, 3, 4, 5, 42, 23, 24, 25] set([0, 1, 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, 41])
total number of confs: 423
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051419 none COCC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)SC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 165, 165, 128, 128, 128, 128, 109, 64, 64, 29, 64, 13, 1, 1, 1, 1, 1, 1, 1, 128, 128, 165, 165, 165, 201, 201, 201, 201, 201, 128, 109, 109, 64, 29, 29, 1, 128, 128, 128, 128, 165] 201
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 790
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051419 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051419
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051419/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051419
Building REAL300025051420
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051420'
/scratch/stefan/7786831/working/building/REAL300025051420 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051420

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051420/0 /scratch/stefan/7786831/working/building/REAL300025051420 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 283)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/283
`/scratch/stefan/7786831/working/3D/283' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C1=NN=NN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051420.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051420.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051420/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051420 none CC(C)C1=NN=NN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 7, 13, 7, 7, 7, 7, 5, 2, 2, 2, 1, 1, 1, 5, 8, 8, 8, 30, 52, 139, 139, 139, 139, 139, 1, 1, 13, 13, 13, 13, 13, 13, 13, 5, 5, 2, 5, 5, 8, 30, 30, 139, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
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: REAL300025051420 none CC(C)C1=NN=NN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 7, 7, 7, 7, 14, 24, 24, 24, 72, 111, 201, 201, 201, 201, 201, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 14, 14, 24, 72, 72, 201, 7, 7, 7, 7] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 538
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051420 none CC(C)C1=NN=NN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 191, 139, 139, 139, 139, 115, 62, 62, 28, 62, 13, 1, 1, 1, 1, 1, 1, 1, 139, 139, 201, 201, 201, 201, 201, 201, 201, 191, 191, 139, 115, 115, 62, 28, 28, 1, 139, 139, 139, 139] 201
rigid atoms, others: [42, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46])
total number of confs: 847
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051420 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051420
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051420/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051420
Building REAL300025051421
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051421'
/scratch/stefan/7786831/working/building/REAL300025051421 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051421

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051421/0 /scratch/stefan/7786831/working/building/REAL300025051421 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 284)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/284
`/scratch/stefan/7786831/working/3D/284' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)OC(C2CC2)=N1)

`REAL300025051421.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051421.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051421/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051421 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)OC(C2CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 2, 2, 1, 1, 1, 4, 6, 6, 6, 20, 29, 113, 113, 113, 113, 113, 1, 1, 4, 4, 4, 35, 35, 4, 4, 4, 4, 2, 4, 4, 6, 20, 20, 113, 1, 1, 1, 1, 35, 35, 35, 35, 35] 201
rigid atoms, others: [37, 6, 7, 40, 39, 19, 20, 38, 5] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45])
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: REAL300025051421 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)OC(C2CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 4, 4, 9, 15, 15, 15, 43, 59, 166, 166, 166, 166, 166, 4, 4, 1, 1, 1, 12, 12, 1, 2, 2, 2, 4, 9, 9, 15, 43, 43, 166, 4, 4, 4, 4, 12, 12, 12, 12, 12] 201
rigid atoms, others: [0, 1, 2, 3, 21, 22, 23, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 392
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051421 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)OC(C2CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 34, 34, 35, 35, 66, 92, 92, 92, 146, 160, 201, 201, 201, 201, 201, 35, 35, 12, 1, 1, 1, 1, 12, 13, 13, 13, 35, 66, 66, 92, 146, 146, 201, 35, 35, 35, 35, 1, 1, 1, 1, 1] 201
rigid atoms, others: [41, 42, 43, 44, 45, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 741
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051421 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)OC(C2CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [166, 166, 113, 113, 113, 113, 85, 49, 49, 23, 49, 12, 1, 1, 1, 1, 1, 1, 1, 113, 113, 166, 166, 166, 201, 201, 166, 166, 166, 166, 113, 85, 85, 49, 23, 23, 1, 113, 113, 113, 113, 201, 201, 201, 201, 201] 201
rigid atoms, others: [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, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 686
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051421 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051421
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051421/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051421
Building REAL300025051422
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051422'
/scratch/stefan/7786831/working/building/REAL300025051422 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051422

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051422/0 /scratch/stefan/7786831/working/building/REAL300025051422 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 285)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/285
`/scratch/stefan/7786831/working/3D/285' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)OC(C(C)C)=N1)

`REAL300025051422.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051422.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051422/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051422 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)OC(C(C)C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 1, 5, 5, 5, 8, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 2, 1, 1, 1, 4, 7, 7, 7, 23, 37, 113, 113, 113, 113, 113, 1, 1, 4, 4, 4, 30, 30, 4, 4, 4, 4, 2, 4, 4, 7, 23, 23, 113, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30] 201
rigid atoms, others: [37, 6, 7, 40, 39, 19, 20, 38, 5] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025051422 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)OC(C(C)C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 1, 5, 5, 5, 8, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 4, 4, 10, 17, 17, 17, 50, 75, 172, 172, 172, 172, 172, 4, 4, 1, 1, 1, 12, 12, 1, 2, 2, 2, 4, 10, 10, 17, 50, 50, 172, 4, 4, 4, 4, 12, 12, 12, 12, 13, 13, 13] 201
rigid atoms, others: [0, 1, 2, 3, 21, 22, 23, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 456
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051422 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)OC(C(C)C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 1, 5, 5, 5, 8, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [172, 172, 113, 113, 113, 113, 83, 47, 47, 22, 47, 12, 1, 1, 1, 1, 1, 1, 1, 113, 113, 172, 172, 172, 201, 201, 172, 172, 172, 172, 113, 83, 83, 47, 22, 22, 1, 113, 113, 113, 113, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [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, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 724
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051422 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051422
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051422/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051422
Building REAL300025051423
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051423'
/scratch/stefan/7786831/working/building/REAL300025051423 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051423

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051423/0 /scratch/stefan/7786831/working/building/REAL300025051423 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 286)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/286
`/scratch/stefan/7786831/working/3D/286' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CNN=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051423.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051423.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051423/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051423 none O=C(CCC1=CNN=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 5, 1, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 3, 6, 6, 6, 12, 15, 22, 22, 22, 22, 22, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 6, 12, 12, 22, 1, 1, 1, 1] 22
rigid atoms, others: [39, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 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: REAL300025051423 none O=C(CCC1=CNN=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 5, 1, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 6, 6, 6, 12, 15, 22, 22, 22, 22, 22, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 6, 12, 12, 22, 2, 2, 2, 2] 22
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 27, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 66
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051423 none O=C(CCC1=CNN=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 5, 1, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 20, 20, 20, 17, 20, 11, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 20, 20, 20, 17, 17, 1, 22, 22, 22, 22] 22
rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 62
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051423 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051423
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051423/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051423
Building REAL300025051424
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051424'
/scratch/stefan/7786831/working/building/REAL300025051424 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051424

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051424/0 /scratch/stefan/7786831/working/building/REAL300025051424 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 287)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/287
`/scratch/stefan/7786831/working/3D/287' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1=CNC=N1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051424.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051424.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051424/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051424 none CC(CC1=CNC=N1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [6, 2, 6, 8, 11, 11, 11, 11, 2, 2, 1, 1, 1, 5, 8, 8, 8, 23, 33, 63, 63, 63, 63, 63, 1, 1, 6, 6, 6, 6, 8, 8, 11, 11, 11, 2, 5, 5, 8, 23, 23, 63, 1, 1, 1, 1] 63
rigid atoms, others: [43, 44, 10, 11, 12, 45, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
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: REAL300025051424 none CC(CC1=CNC=N1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [6, 5, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 11, 13, 18, 18, 18, 32, 39, 63, 63, 63, 63, 63, 11, 11, 6, 6, 6, 6, 5, 5, 1, 1, 1, 11, 13, 13, 18, 32, 32, 63, 11, 11, 11, 11] 63
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 191
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051424 none CC(CC1=CNC=N1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 62, 51, 51, 27, 51, 13, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 62, 62, 51, 27, 27, 1, 63, 63, 63, 63] 63
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 214
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051424 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051424/1 /scratch/stefan/7786831/working/building/REAL300025051424 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 288)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/288
`/scratch/stefan/7786831/working/3D/288' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1=CN=CN1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051424.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051424.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051424/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051424 none CC(CC1=CN=CN1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 2, 6, 15, 17, 17, 17, 17, 2, 2, 1, 1, 1, 4, 8, 8, 8, 23, 36, 104, 104, 104, 104, 104, 1, 1, 6, 6, 6, 6, 15, 15, 17, 17, 17, 2, 4, 4, 8, 23, 23, 104, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
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: REAL300025051424 none CC(CC1=CN=CN1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 3, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 17, 32, 49, 49, 49, 95, 125, 201, 201, 201, 201, 201, 17, 17, 7, 7, 7, 7, 3, 3, 1, 1, 1, 17, 32, 32, 49, 95, 95, 201, 17, 17, 17, 17] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 624
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051424 none CC(CC1=CN=CN1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [170, 104, 170, 193, 201, 201, 201, 201, 104, 104, 104, 90, 61, 61, 28, 61, 12, 1, 1, 1, 1, 1, 1, 1, 104, 104, 170, 170, 170, 170, 193, 193, 201, 201, 201, 104, 90, 90, 61, 28, 28, 1, 104, 104, 104, 104] 201
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 885
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051424 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051424
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051424/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051424/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051424
Building REAL300025051425
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051425'
/scratch/stefan/7786831/working/building/REAL300025051425 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051425

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051425/0 /scratch/stefan/7786831/working/building/REAL300025051425 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 289)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/289
`/scratch/stefan/7786831/working/3D/289' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCCN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=N1)

`REAL300025051425.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051425.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051425/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051425 none C=CCCN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=N1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 15, 9, 3, 3, 3, 2, 2, 2, 1, 1, 1, 4, 7, 7, 7, 21, 29, 106, 106, 106, 106, 106, 1, 1, 3, 3, 23, 23, 23, 15, 15, 9, 9, 3, 2, 4, 4, 7, 21, 21, 106, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 283
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051425 none C=CCCN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=N1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 14, 8, 1, 1, 1, 1, 1, 2, 2, 3, 3, 6, 9, 9, 9, 26, 35, 115, 115, 115, 115, 115, 3, 3, 1, 1, 22, 22, 22, 14, 14, 8, 8, 1, 3, 6, 6, 9, 26, 26, 115, 3, 3, 3, 3] 201
rigid atoms, others: [34, 3, 4, 5, 6, 7, 25, 26] set([0, 1, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 314
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051425 none C=CCCN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=N1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 186, 115, 115, 115, 106, 106, 106, 106, 82, 50, 50, 26, 50, 13, 1, 1, 1, 1, 1, 1, 1, 106, 106, 115, 115, 201, 201, 201, 201, 201, 186, 186, 115, 106, 82, 82, 50, 26, 26, 1, 106, 106, 106, 106] 201
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 876
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051425 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051425
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051425/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051425
Building REAL300025051426
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051426'
/scratch/stefan/7786831/working/building/REAL300025051426 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051426

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051426/0 /scratch/stefan/7786831/working/building/REAL300025051426 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 290)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/290
`/scratch/stefan/7786831/working/3D/290' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2CC2)CC1)

`REAL300025051426.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051426.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051426/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051426 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 21, 26, 58, 58, 58, 58, 58, 5, 1, 1, 1, 3, 3, 3, 25, 25, 25, 25, 25, 75, 75, 1, 1, 21, 21, 58, 10, 5, 5, 3, 25, 25, 75, 75, 75, 75, 75, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 331
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051426 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [41, 20, 12, 1, 1, 1, 1, 1, 1, 1, 41, 41, 54, 58, 58, 58, 58, 182, 182, 182, 182, 182, 201, 201, 58, 58, 20, 20, 1, 41, 54, 54, 58, 182, 182, 201, 201, 201, 201, 201, 58, 58, 58, 58] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 632
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051426 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [143, 143, 143, 175, 180, 201, 201, 201, 201, 201, 99, 75, 53, 53, 8, 53, 8, 8, 8, 1, 8, 1, 1, 1, 75, 75, 175, 175, 201, 143, 99, 99, 53, 8, 8, 1, 1, 1, 1, 1, 75, 75, 75, 75] 201
rigid atoms, others: [35, 36, 37, 38, 39, 19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43])
total number of confs: 724
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051426 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [77, 77, 77, 112, 123, 182, 182, 182, 182, 182, 42, 25, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 8, 8, 25, 25, 112, 112, 182, 77, 42, 42, 13, 1, 1, 8, 8, 8, 8, 8, 25, 25, 25, 25] 201
rigid atoms, others: [33, 34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 608
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051426 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051426
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051426/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051426
Building REAL300025051427
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051427'
/scratch/stefan/7786831/working/building/REAL300025051427 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051427

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051427/0 /scratch/stefan/7786831/working/building/REAL300025051427 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 291)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/291
`/scratch/stefan/7786831/working/3D/291' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCC3CCC[N@@H+]32)CC1)

`REAL300025051427.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051427.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051427/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051427 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCC3CCC[N@@H+]32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 6, 6, 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: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [10, 10, 10, 14, 15, 21, 21, 21, 21, 21, 4, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 14, 14, 21, 10, 4, 4, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1] 22
rigid atoms, others: [11, 12, 13, 49, 50, 51, 52, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 86
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051427 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCC3CCC[N@@H+]32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 6, 6, 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: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [20, 13, 10, 1, 1, 1, 1, 1, 1, 1, 20, 20, 21, 21, 21, 21, 21, 22, 22, 22, 22, 22, 22, 22, 22, 22, 21, 21, 13, 13, 1, 20, 21, 21, 21, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 21, 21, 21, 21] 22
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 58
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051427 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCC3CCC[N@@H+]32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 6, 6, 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: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [14, 14, 14, 17, 18, 22, 22, 22, 22, 22, 10, 9, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 17, 17, 22, 14, 10, 10, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9] 22
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 49, 50, 51, 52])
total number of confs: 72
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051427 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051427/1 /scratch/stefan/7786831/working/building/REAL300025051427 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 292)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/292
`/scratch/stefan/7786831/working/3D/292' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCC3CCC[N@H+]32)CC1)

`REAL300025051427.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051427.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051427/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051427 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCC3CCC[N@H+]32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 6, 6, 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: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [16, 16, 16, 25, 27, 31, 31, 31, 31, 31, 6, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 25, 25, 31, 16, 6, 6, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1] 32
rigid atoms, others: [11, 12, 13, 49, 50, 51, 52, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 120
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051427 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCC3CCC[N@H+]32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 6, 6, 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: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [27, 18, 11, 1, 1, 1, 1, 1, 1, 1, 27, 27, 30, 31, 31, 31, 31, 32, 32, 32, 32, 32, 32, 32, 32, 32, 31, 31, 18, 18, 1, 27, 30, 30, 31, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 31, 31, 31, 31] 32
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 114
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051427 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCC3CCC[N@H+]32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 6, 6, 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: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [18, 18, 18, 26, 28, 32, 32, 32, 32, 32, 8, 5, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 26, 26, 32, 18, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 32
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 49, 50, 51, 52])
total number of confs: 110
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051427 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051427
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051427/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051427/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051427
Building REAL300025051428
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051428'
/scratch/stefan/7786831/working/building/REAL300025051428 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051428

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051428/0 /scratch/stefan/7786831/working/building/REAL300025051428 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 293)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/293
`/scratch/stefan/7786831/working/3D/293' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2CCC2)CC1)

`REAL300025051428.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051428.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051428/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051428 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 15, 41, 45, 97, 97, 97, 97, 97, 5, 1, 1, 1, 3, 3, 3, 24, 24, 24, 24, 24, 51, 51, 51, 1, 1, 41, 41, 97, 15, 5, 5, 3, 24, 24, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
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: REAL300025051428 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [39, 25, 12, 1, 1, 1, 1, 1, 1, 1, 39, 39, 77, 97, 97, 97, 97, 201, 201, 201, 201, 201, 201, 201, 201, 97, 97, 25, 25, 1, 39, 77, 77, 97, 201, 201, 201, 201, 201, 201, 201, 201, 201, 97, 97, 97, 97] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46])
total number of confs: 700
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051428 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [122, 122, 122, 175, 179, 201, 201, 201, 201, 201, 63, 51, 31, 31, 4, 31, 4, 4, 4, 1, 4, 1, 1, 1, 1, 51, 51, 175, 175, 201, 122, 63, 63, 31, 4, 4, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 19, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46])
total number of confs: 737
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051428 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [89, 89, 89, 162, 169, 201, 201, 201, 201, 201, 35, 24, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 4, 4, 4, 24, 24, 162, 162, 201, 89, 35, 35, 13, 1, 1, 4, 4, 4, 4, 4, 4, 4, 24, 24, 24, 24] 201
rigid atoms, others: [34, 35, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 745
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051428 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051428
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051428/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051428
Building REAL300025051429
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051429'
/scratch/stefan/7786831/working/building/REAL300025051429 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051429

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051429/0 /scratch/stefan/7786831/working/building/REAL300025051429 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 294)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/294
`/scratch/stefan/7786831/working/3D/294' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3NC=CC=C23)CC1)

`REAL300025051429.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051429.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051429/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051429 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3NC=CC=C23)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 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: [19, 19, 19, 68, 87, 166, 166, 166, 166, 166, 5, 1, 1, 1, 3, 3, 3, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 68, 68, 166, 19, 5, 5, 3, 16, 16, 16, 16, 16, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 420
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051429 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3NC=CC=C23)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 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: [70, 32, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 133, 166, 166, 166, 166, 201, 201, 201, 201, 201, 201, 201, 201, 166, 166, 32, 32, 1, 70, 133, 133, 166, 201, 201, 201, 201, 201, 166, 166, 166, 166] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 685
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051429 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3NC=CC=C23)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 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: [67, 67, 67, 140, 152, 201, 201, 201, 201, 201, 23, 16, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 140, 140, 201, 67, 23, 23, 10, 1, 1, 1, 1, 1, 16, 16, 16, 16] 201
rigid atoms, others: [34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42])
total number of confs: 661
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051429 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051429
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051429/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051429
Building REAL300025051430
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051430'
/scratch/stefan/7786831/working/building/REAL300025051430 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051430

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051430/0 /scratch/stefan/7786831/working/building/REAL300025051430 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 295)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/295
`/scratch/stefan/7786831/working/3D/295' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCN1C=CC=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051430.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051430.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051430/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051430 none O=C(CCCN1C=CC=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 1, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 10, 14, 24, 31, 31, 31, 31, 1, 1, 1, 4, 7, 7, 7, 22, 36, 88, 88, 88, 88, 88, 1, 1, 10, 10, 17, 17, 22, 23, 31, 31, 31, 2, 4, 4, 7, 22, 22, 88, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
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: REAL300025051430 none O=C(CCCN1C=CC=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 1, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 18, 9, 5, 1, 1, 1, 1, 1, 1, 31, 31, 31, 38, 48, 48, 48, 94, 118, 201, 201, 201, 201, 201, 31, 31, 18, 18, 9, 9, 5, 5, 1, 1, 1, 31, 38, 38, 48, 94, 94, 201, 31, 31, 31, 31] 201
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 638
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051430 none O=C(CCCN1C=CC=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 1, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 154, 150, 176, 201, 201, 201, 201, 88, 73, 56, 56, 28, 56, 13, 1, 1, 1, 1, 1, 1, 1, 88, 88, 154, 154, 167, 167, 169, 166, 201, 201, 201, 88, 73, 73, 56, 28, 28, 1, 88, 88, 88, 88] 201
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 866
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051430 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051430
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051430/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051430
Building REAL300025051431
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051431'
/scratch/stefan/7786831/working/building/REAL300025051431 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051431

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051431/0 /scratch/stefan/7786831/working/building/REAL300025051431 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 296)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/296
`/scratch/stefan/7786831/working/3D/296' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)CC(=O)NCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051431.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051431.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051431/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051431 none CC(C)(C)CC(=O)NCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [95, 95, 95, 95, 88, 88, 88, 88, 83, 83, 83, 83, 73, 59, 59, 37, 59, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 88, 88, 88, 83, 73, 73, 59, 37, 37, 1, 83, 83, 83, 83] 95
rigid atoms, others: [47, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51])
total number of confs: 382
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051431 none CC(C)(C)CC(=O)NCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 8, 8, 5, 5, 5, 4, 2, 2, 2, 1, 1, 1, 7, 23, 23, 23, 43, 53, 83, 83, 83, 83, 83, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 4, 4, 2, 7, 7, 23, 43, 43, 83, 1, 1, 1, 1] 95
rigid atoms, others: [11, 12, 13, 48, 49, 50, 51, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 254
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051431 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051431
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051431/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051431
Building REAL300025051432
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051432'
/scratch/stefan/7786831/working/building/REAL300025051432 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051432

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051432/0 /scratch/stefan/7786831/working/building/REAL300025051432 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 297)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/297
`/scratch/stefan/7786831/working/3D/297' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=NC=CS1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051432.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051432.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051432/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051432 none O=C(CCC1=NC=CS1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 1, 14, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 10, 17, 27, 27, 27, 27, 1, 1, 1, 5, 10, 10, 10, 31, 50, 126, 126, 126, 126, 126, 1, 1, 10, 10, 17, 17, 27, 27, 2, 5, 5, 10, 31, 31, 126, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 353
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051432 none O=C(CCC1=NC=CS1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 1, 14, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 8, 3, 1, 1, 1, 1, 1, 1, 27, 27, 27, 46, 64, 64, 64, 107, 134, 201, 201, 201, 201, 201, 27, 27, 8, 8, 3, 3, 1, 1, 27, 46, 46, 64, 107, 107, 201, 27, 27, 27, 27] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 29, 30] set([0, 1, 2, 9, 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])
total number of confs: 648
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051432 none O=C(CCC1=NC=CS1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 1, 14, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [126, 126, 126, 179, 185, 201, 201, 201, 201, 126, 110, 63, 63, 27, 63, 13, 1, 1, 1, 1, 1, 1, 1, 126, 126, 179, 179, 185, 185, 201, 201, 126, 110, 110, 63, 27, 27, 1, 126, 126, 126, 126] 201
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41])
total number of confs: 814
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051432 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051432
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051432/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051432
Building REAL300025051433
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051433'
/scratch/stefan/7786831/working/building/REAL300025051433 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051433

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051433/0 /scratch/stefan/7786831/working/building/REAL300025051433 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 298)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/298
`/scratch/stefan/7786831/working/3D/298' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCC(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051433.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051433.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051433/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051433 none COCCC(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 193, 116, 193, 116, 116, 116, 98, 69, 69, 31, 69, 13, 1, 1, 1, 1, 1, 1, 1, 116, 116, 201, 201, 201, 201, 201, 201, 201, 193, 193, 193, 193, 116, 98, 98, 69, 31, 31, 1, 116, 116, 116, 116] 201
rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 892
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051433 none COCCC(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 14, 13, 7, 2, 7, 2, 2, 1, 1, 1, 3, 6, 6, 6, 22, 41, 116, 116, 116, 116, 116, 1, 1, 26, 26, 26, 14, 14, 13, 13, 7, 7, 7, 7, 2, 3, 3, 6, 22, 22, 116, 1, 1, 1, 1] 201
rigid atoms, others: [8, 9, 10, 43, 44, 45, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
total number of confs: 295
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051433 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051433
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051433/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051433
Building REAL300025051434
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051434'
/scratch/stefan/7786831/working/building/REAL300025051434 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051434

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051434/0 /scratch/stefan/7786831/working/building/REAL300025051434 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 299)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/299
`/scratch/stefan/7786831/working/3D/299' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1OC(C)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1C)

`REAL300025051434.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051434.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051434/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051434 none CC1OC(C)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 6, 23, 23, 23, 74, 97, 188, 188, 188, 188, 188, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 23, 74, 74, 188, 1, 1, 1, 1, 3, 3, 3, 3] 201
rigid atoms, others: [8, 9, 10, 43, 44, 45, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 46, 47, 48, 49])
total number of confs: 473
number of broken/clashed sets: 70
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051434 none CC1OC(C)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 10, 36, 36, 36, 99, 122, 201, 201, 201, 201, 201, 3, 3, 1, 1, 2, 2, 2, 1, 1, 2, 2, 2, 1, 3, 10, 10, 36, 99, 99, 201, 3, 3, 3, 3, 1, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 46, 24, 25, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49])
total number of confs: 582
number of broken/clashed sets: 70
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051434 none CC1OC(C)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 188, 188, 188, 188, 144, 68, 68, 28, 68, 13, 1, 1, 1, 1, 1, 1, 1, 188, 188, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 188, 144, 144, 68, 28, 28, 1, 188, 188, 188, 188, 201, 201, 201, 201] 201
rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 759
number of broken/clashed sets: 70
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051434 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051434
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051434/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051434
Building REAL300025051435
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051435'
/scratch/stefan/7786831/working/building/REAL300025051435 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051435

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051435/0 /scratch/stefan/7786831/working/building/REAL300025051435 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 300)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/300
`/scratch/stefan/7786831/working/3D/300' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=CC(F)=C1)

`REAL300025051435.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051435.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051435/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051435 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=CC(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [175, 144, 144, 144, 144, 103, 59, 59, 29, 59, 13, 1, 1, 1, 1, 1, 1, 1, 144, 144, 175, 201, 201, 201, 201, 201, 201, 175, 175, 175, 175, 144, 103, 103, 59, 29, 29, 1, 144, 144, 144, 144, 201, 201, 201, 201] 201
rigid atoms, others: [37, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 770
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051435 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=CC(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 2, 2, 2, 1, 1, 1, 7, 20, 20, 20, 54, 63, 144, 144, 144, 144, 144, 1, 1, 5, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 2, 7, 7, 20, 54, 54, 144, 1, 1, 1, 1, 8, 8, 8, 8] 201
rigid atoms, others: [4, 5, 38, 39, 40, 41, 18, 19, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45])
total number of confs: 366
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051435 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=CC(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 8, 8, 8, 8, 19, 43, 43, 43, 93, 112, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 8, 19, 19, 43, 93, 93, 201, 8, 8, 8, 8, 1, 1, 1, 1] 201
rigid atoms, others: [1, 42, 43, 44, 45, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 560
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051435 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051435
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051435/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051435
Building REAL300025051436
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051436'
/scratch/stefan/7786831/working/building/REAL300025051436 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051436

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051436/0 /scratch/stefan/7786831/working/building/REAL300025051436 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 301)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/301
`/scratch/stefan/7786831/working/3D/301' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCS2(=O)=O)CC1)

`REAL300025051436.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051436.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051436/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051436 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCS2(=O)=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
142  conformations in input
total number of sets (complete confs): 142
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 65, 77, 136, 136, 136, 136, 136, 5, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 1, 1, 65, 65, 136, 22, 5, 5, 3, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1] 142
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 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: REAL300025051436 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCS2(=O)=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
142  conformations in input
total number of sets (complete confs): 142
using faster count positions algorithm for large data
unique positions, atoms: [70, 33, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 117, 136, 136, 136, 136, 142, 142, 142, 142, 142, 142, 136, 136, 33, 33, 1, 70, 117, 117, 136, 142, 142, 142, 142, 142, 142, 142, 136, 136, 136, 136] 142
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 546
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051436 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCS2(=O)=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
142  conformations in input
total number of sets (complete confs): 142
using faster count positions algorithm for large data
unique positions, atoms: [44, 44, 44, 97, 106, 142, 142, 142, 142, 142, 14, 8, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 97, 97, 142, 44, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 142
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42])
total number of confs: 449
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051436 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051436
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051436/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051436
Building REAL300025051437
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051437'
/scratch/stefan/7786831/working/building/REAL300025051437 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051437

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051437/0 /scratch/stefan/7786831/working/building/REAL300025051437 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 302)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/302
`/scratch/stefan/7786831/working/3D/302' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NOC3=C2COCC3)CC1)

`REAL300025051437.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051437.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051437/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051437 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NOC3=C2COCC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 12, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [29, 29, 29, 95, 102, 201, 201, 201, 201, 201, 6, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 95, 95, 201, 29, 6, 6, 3, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
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: REAL300025051437 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NOC3=C2COCC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 12, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [58, 32, 13, 1, 1, 1, 1, 1, 1, 1, 58, 58, 130, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 32, 32, 1, 58, 130, 130, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 732
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051437 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NOC3=C2COCC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 12, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [49, 49, 49, 124, 130, 201, 201, 201, 201, 201, 10, 5, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 124, 124, 201, 49, 10, 10, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43])
total number of confs: 610
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051437 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051437
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051437/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051437
Building REAL300025051438
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051438'
/scratch/stefan/7786831/working/building/REAL300025051438 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051438

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051438/0 /scratch/stefan/7786831/working/building/REAL300025051438 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 303)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/303
`/scratch/stefan/7786831/working/3D/303' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3=CNN=C3C2)CC1)

`REAL300025051438.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051438.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051438/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051438 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3=CNN=C3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 8, 8, 1, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 19, 53, 65, 151, 151, 151, 151, 151, 5, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 53, 53, 151, 19, 5, 5, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 368
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051438 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3=CNN=C3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 8, 8, 1, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 34, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 126, 151, 151, 151, 151, 201, 201, 201, 201, 201, 201, 201, 201, 151, 151, 34, 34, 1, 71, 126, 126, 151, 201, 201, 201, 201, 201, 201, 201, 201, 201, 151, 151, 151, 151] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46])
total number of confs: 743
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051438 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3=CNN=C3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 8, 8, 1, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 133, 146, 201, 201, 201, 201, 201, 24, 14, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 133, 133, 201, 67, 24, 24, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46])
total number of confs: 665
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051438 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051438
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051438/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051438
Building REAL300025051439
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051439'
/scratch/stefan/7786831/working/building/REAL300025051439 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300025051439

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051439/0 /scratch/stefan/7786831/working/building/REAL300025051439 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 304)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/304
`/scratch/stefan/7786831/working/3D/304' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1CCOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025051439.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051439.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051439/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051439 none CCN1CCOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 7, 21, 21, 21, 51, 60, 156, 157, 157, 157, 157, 1, 1, 5, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 2, 7, 7, 21, 51, 51, 157, 1, 1, 1, 1, 5, 5] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 46, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48])
total number of confs: 396
number of broken/clashed sets: 45
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051439 none CCN1CCOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 18, 40, 40, 40, 85, 98, 201, 201, 201, 201, 201, 5, 5, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 5, 18, 18, 40, 85, 85, 201, 5, 5, 5, 5, 1, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 47, 48, 35, 25, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 550
number of broken/clashed sets: 45
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051439 none CCN1CCOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 157, 157, 157, 157, 105, 52, 52, 27, 52, 13, 1, 1, 1, 1, 1, 1, 1, 157, 157, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 157, 105, 105, 52, 27, 27, 1, 157, 157, 157, 157, 201, 201] 201
rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48])
total number of confs: 758
number of broken/clashed sets: 45
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051439 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051439/1 /scratch/stefan/7786831/working/building/REAL300025051439 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 305)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/305
`/scratch/stefan/7786831/working/3D/305' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[N@@H+]1CCOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025051439.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051439.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051439/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051439 none CC[N@@H+]1CCOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [5, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 5, 12, 12, 12, 23, 27, 48, 48, 48, 48, 48, 1, 1, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 2, 5, 5, 12, 23, 23, 48, 1, 1, 1, 1, 3, 3] 49
rigid atoms, others: [44, 10, 11, 12, 45, 46, 47, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49])
total number of confs: 152
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: REAL300025051439 none CC[N@@H+]1CCOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 7, 15, 15, 15, 28, 31, 49, 49, 49, 49, 49, 3, 3, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 7, 7, 15, 28, 28, 49, 3, 3, 3, 3, 1, 1] 49
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 7, 34, 48, 49, 35, 36, 26] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 160
number of broken/clashed sets: 48
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051439 none CC[N@@H+]1CCOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 48, 48, 48, 48, 44, 36, 36, 22, 36, 13, 1, 1, 1, 1, 1, 1, 1, 48, 48, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 48, 44, 44, 36, 22, 22, 1, 48, 48, 48, 48, 49, 49] 49
rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49])
total number of confs: 170
number of broken/clashed sets: 48
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051439 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `2'
/scratch/stefan/7786831/working/building/REAL300025051439/2 /scratch/stefan/7786831/working/building/REAL300025051439 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 2 (index: 306)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/306
`/scratch/stefan/7786831/working/3D/306' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[N@H+]1CCOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025051439.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300025051439.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051439/2/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`2.mol2' -> `2.mol2.original'
`output.mol2' -> `2.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051439 none CC[N@H+]1CCOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [5, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 3, 6, 6, 6, 13, 16, 26, 26, 26, 26, 26, 1, 1, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 2, 3, 3, 6, 13, 13, 26, 1, 1, 1, 1, 3, 3] 26
rigid atoms, others: [44, 10, 11, 12, 45, 46, 47, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49])
total number of confs: 97
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: REAL300025051439 none CC[N@H+]1CCOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 3, 3, 3, 3, 4, 7, 7, 7, 13, 16, 26, 26, 26, 26, 26, 3, 3, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 4, 4, 7, 13, 13, 26, 3, 3, 3, 3, 1, 1] 26
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 7, 34, 48, 49, 35, 36, 26] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 86
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051439 none CC[N@H+]1CCOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 23, 19, 19, 12, 19, 8, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 23, 23, 19, 12, 12, 1, 26, 26, 26, 26, 26, 26] 26
rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49])
total number of confs: 90
number of broken/clashed sets: 25
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051439 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051439
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
2: /scratch/stefan/7786831/working/building/REAL300025051439/2.*
1: /scratch/stefan/7786831/working/building/REAL300025051439/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051439/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051439
Building REAL300025051440
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051440'
/scratch/stefan/7786831/working/building/REAL300025051440 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051440

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051440/0 /scratch/stefan/7786831/working/building/REAL300025051440 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 307)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/307
`/scratch/stefan/7786831/working/3D/307' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCC(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1)

`REAL300025051440.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051440.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051440/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051440 none CC1CCC(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 19, 19, 12, 10, 2, 2, 2, 1, 1, 1, 4, 6, 6, 6, 22, 34, 114, 114, 114, 114, 114, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 13, 13, 10, 10, 2, 4, 4, 6, 22, 22, 114, 1, 1, 1, 1] 201
rigid atoms, others: [9, 10, 11, 46, 47, 48, 49, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 291
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051440 none CC1CCC(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 9, 19, 19, 19, 19, 36, 51, 51, 51, 96, 124, 201, 201, 201, 201, 201, 19, 19, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 19, 36, 36, 51, 96, 96, 201, 19, 19, 19, 19] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 25, 5, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 619
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051440 none CC1CCC(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 197, 114, 114, 114, 114, 102, 65, 65, 27, 65, 13, 1, 1, 1, 1, 1, 1, 1, 114, 114, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 197, 197, 114, 102, 102, 65, 27, 27, 1, 114, 114, 114, 114] 201
rigid atoms, others: [45, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49])
total number of confs: 869
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051440 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051440
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051440/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051440
Building REAL300025051441
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051441'
/scratch/stefan/7786831/working/building/REAL300025051441 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051441

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051441/0 /scratch/stefan/7786831/working/building/REAL300025051441 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 308)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/308
`/scratch/stefan/7786831/working/3D/308' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](CC1=CC=CC=C1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051441.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051441.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051441/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051441 none C[C@@H](CC1=CC=CC=C1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 5, 6, 6, 6, 6, 6, 6, 2, 2, 1, 1, 1, 7, 20, 20, 20, 64, 77, 138, 138, 138, 138, 138, 1, 1, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 2, 7, 7, 20, 64, 64, 138, 1, 1, 1, 1] 201
rigid atoms, others: [47, 12, 13, 14, 45, 48, 46, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 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: REAL300025051441 none C[C@@H](CC1=CC=CC=C1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 6, 6, 6, 6, 17, 38, 38, 38, 106, 123, 201, 201, 201, 201, 201, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 17, 17, 38, 106, 106, 201, 6, 6, 6, 6] 201
rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 8, 9, 7, 35, 36, 37, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 593
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051441 none C[C@@H](CC1=CC=CC=C1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [198, 138, 198, 198, 201, 201, 201, 201, 201, 201, 138, 138, 138, 120, 54, 54, 28, 54, 13, 1, 1, 1, 1, 1, 1, 1, 138, 138, 198, 198, 198, 201, 201, 201, 201, 201, 201, 201, 138, 120, 120, 54, 28, 28, 1, 138, 138, 138, 138] 201
rigid atoms, others: [44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48])
total number of confs: 891
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051441 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051441
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051441/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051441
Building REAL300025051442
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051442'
/scratch/stefan/7786831/working/building/REAL300025051442 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051442

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051442/0 /scratch/stefan/7786831/working/building/REAL300025051442 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 309)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/309
`/scratch/stefan/7786831/working/3D/309' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CC1=CC=CC=C1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051442.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051442.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051442/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051442 none C[C@H](CC1=CC=CC=C1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 5, 6, 6, 6, 6, 6, 6, 2, 2, 1, 1, 1, 7, 20, 20, 20, 65, 88, 176, 176, 176, 176, 176, 1, 1, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 2, 7, 7, 20, 65, 65, 176, 1, 1, 1, 1] 201
rigid atoms, others: [47, 12, 13, 14, 45, 48, 46, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 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: REAL300025051442 none C[C@H](CC1=CC=CC=C1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 4, 6, 6, 6, 6, 16, 41, 41, 41, 101, 125, 201, 201, 201, 201, 201, 6, 6, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 16, 16, 41, 101, 101, 201, 6, 6, 6, 6] 201
rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 8, 9, 7, 35, 36, 37, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 595
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051442 none C[C@H](CC1=CC=CC=C1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 176, 201, 201, 201, 201, 201, 201, 201, 201, 176, 176, 176, 133, 61, 61, 30, 61, 13, 1, 1, 1, 1, 1, 1, 1, 176, 176, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 176, 133, 133, 61, 30, 30, 1, 176, 176, 176, 176] 201
rigid atoms, others: [44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48])
total number of confs: 829
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051442 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051442
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051442/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051442
Building REAL300025051443
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051443'
/scratch/stefan/7786831/working/building/REAL300025051443 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051443

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051443/0 /scratch/stefan/7786831/working/building/REAL300025051443 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 310)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/310
`/scratch/stefan/7786831/working/3D/310' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCCC(CC)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051443.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051443.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051443/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051443 none CCCCCC(CC)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 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.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 170, 104, 170, 168, 104, 104, 104, 90, 64, 64, 48, 64, 13, 1, 1, 1, 1, 1, 1, 1, 104, 104, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 170, 170, 170, 170, 170, 170, 104, 90, 90, 64, 48, 48, 1, 104, 104, 104, 104] 201
rigid atoms, others: [49, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53])
total number of confs: 936
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051443 none CCCCCC(CC)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 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.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 6, 2, 6, 6, 2, 2, 1, 1, 1, 4, 11, 11, 11, 31, 46, 104, 104, 104, 104, 104, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 7, 7, 7, 7, 7, 2, 4, 4, 11, 31, 31, 104, 1, 1, 1, 1] 201
rigid atoms, others: [10, 11, 12, 50, 51, 52, 53, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 299
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051443 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051443
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051443/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051443
Building REAL300025051444
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051444'
/scratch/stefan/7786831/working/building/REAL300025051444 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051444

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051444/0 /scratch/stefan/7786831/working/building/REAL300025051444 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 311)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/311
`/scratch/stefan/7786831/working/3D/311' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(C3CC3)C=C2)CC1)

`REAL300025051444.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051444.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051444/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051444 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(C3CC3)C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 16, 16, 47, 54, 110, 110, 110, 110, 110, 5, 1, 1, 1, 3, 3, 3, 5, 5, 3, 3, 9, 9, 5, 5, 1, 1, 47, 47, 110, 16, 5, 5, 3, 5, 5, 9, 9, 9, 9, 9, 5, 5, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 308
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051444 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(C3CC3)C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [60, 30, 13, 1, 1, 1, 1, 1, 1, 1, 60, 60, 98, 110, 110, 110, 110, 137, 137, 110, 110, 201, 201, 137, 137, 110, 110, 30, 30, 1, 60, 98, 98, 110, 137, 137, 201, 201, 201, 201, 201, 137, 137, 110, 110, 110, 110] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46])
total number of confs: 875
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051444 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(C3CC3)C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [54, 54, 54, 140, 154, 201, 201, 201, 201, 201, 17, 9, 5, 5, 3, 5, 3, 3, 3, 1, 1, 1, 1, 3, 3, 9, 9, 140, 140, 201, 54, 17, 17, 5, 3, 3, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9, 9] 201
rigid atoms, others: [36, 37, 38, 39, 40, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46])
total number of confs: 669
number of broken/clashed sets: 1
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051444 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(C3CC3)C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 28, 28, 78, 87, 137, 137, 137, 137, 137, 9, 5, 3, 3, 1, 3, 1, 1, 1, 1, 1, 3, 3, 1, 1, 5, 5, 78, 78, 137, 28, 9, 9, 3, 1, 1, 3, 3, 3, 3, 3, 1, 1, 5, 5, 5, 5] 201
rigid atoms, others: [34, 35, 41, 42, 14, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 43, 44, 45, 46])
total number of confs: 414
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051444 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051444
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051444/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051444
Building REAL300025051445
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051445'
/scratch/stefan/7786831/working/building/REAL300025051445 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051445

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051445/0 /scratch/stefan/7786831/working/building/REAL300025051445 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 312)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/312
`/scratch/stefan/7786831/working/3D/312' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)N1CCCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025051445.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051445.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051445/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051445 none NC(=O)N1CCCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 8, 18, 8, 8, 8, 8, 2, 2, 2, 1, 1, 1, 4, 7, 7, 7, 24, 38, 111, 111, 111, 111, 111, 1, 1, 8, 18, 18, 8, 8, 8, 8, 8, 8, 8, 2, 4, 4, 7, 24, 24, 111, 1, 1, 1, 1, 8, 8] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48])
total number of confs: 269
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: REAL300025051445 none NC(=O)N1CCCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 18, 27, 27, 27, 65, 92, 190, 190, 190, 190, 190, 8, 8, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 8, 18, 18, 27, 65, 65, 190, 8, 8, 8, 8, 1, 1] 201
rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 47, 33, 35, 48, 26, 29, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 486
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051445 none NC(=O)N1CCCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 190, 201, 190, 190, 190, 190, 111, 111, 111, 111, 89, 58, 58, 28, 58, 13, 1, 1, 1, 1, 1, 1, 1, 111, 111, 190, 201, 201, 190, 190, 190, 190, 190, 190, 190, 111, 89, 89, 58, 28, 28, 1, 111, 111, 111, 111, 190, 190] 201
rigid atoms, others: [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, 40, 41, 43, 44, 45, 46, 47, 48])
total number of confs: 732
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051445 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051445
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051445/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051445
Building REAL300025051446
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051446'
/scratch/stefan/7786831/working/building/REAL300025051446 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051446

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051446/0 /scratch/stefan/7786831/working/building/REAL300025051446 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 313)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/313
`/scratch/stefan/7786831/working/3D/313' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1F)

`REAL300025051446.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051446.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051446/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051446 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 18, 18, 18, 54, 63, 99, 99, 99, 99, 99, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 18, 54, 54, 99, 1, 1, 1, 1, 5] 201
rigid atoms, others: [38, 7, 8, 9, 39, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 42])
total number of confs: 291
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051446 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 65, 65, 65, 136, 156, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 2, 2, 2, 1, 1, 5, 13, 13, 65, 136, 136, 201, 5, 5, 5, 5, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 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])
total number of confs: 647
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051446 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 99, 99, 99, 99, 78, 51, 51, 23, 51, 13, 1, 1, 1, 1, 1, 1, 1, 99, 99, 201, 201, 201, 201, 201, 201, 201, 201, 99, 78, 78, 51, 23, 23, 1, 99, 99, 99, 99, 201] 201
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 526
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051446 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051446
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051446/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051446
Building REAL300025051447
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051447'
/scratch/stefan/7786831/working/building/REAL300025051447 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051447

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051447/0 /scratch/stefan/7786831/working/building/REAL300025051447 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 314)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/314
`/scratch/stefan/7786831/working/3D/314' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=C1C)

`REAL300025051447.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051447.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051447/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051447 none COC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 14, 14, 14, 42, 59, 126, 126, 126, 126, 126, 1, 1, 5, 5, 5, 5, 13, 13, 13, 5, 2, 4, 4, 14, 42, 42, 126, 1, 1, 1, 1, 5, 5, 5, 5, 5] 201
rigid atoms, others: [38, 7, 8, 9, 39, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 42, 43, 44, 45, 46])
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: REAL300025051447 none COC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 37, 37, 37, 91, 118, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 1, 4, 4, 4, 1, 5, 12, 12, 37, 91, 91, 201, 5, 5, 5, 5, 1, 1, 2, 2, 2] 201
rigid atoms, others: [1, 2, 3, 4, 5, 42, 43, 23, 24, 25, 26, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46])
total number of confs: 560
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051447 none COC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 126, 126, 126, 126, 103, 71, 71, 33, 71, 13, 1, 1, 1, 1, 1, 1, 1, 126, 126, 201, 201, 201, 201, 201, 201, 201, 201, 126, 103, 103, 71, 33, 33, 1, 126, 126, 126, 126, 201, 201, 201, 201, 201] 201
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 602
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051447 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051447
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051447/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051447
Building REAL300025051448
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051448'
/scratch/stefan/7786831/working/building/REAL300025051448 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051448

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051448/0 /scratch/stefan/7786831/working/building/REAL300025051448 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 315)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/315
`/scratch/stefan/7786831/working/3D/315' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(Cl)=CC=C2F)CC1)

`REAL300025051448.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051448.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051448/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051448 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(Cl)=CC=C2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 90, 107, 191, 191, 191, 191, 191, 6, 1, 1, 1, 3, 3, 3, 9, 9, 9, 4, 9, 9, 9, 1, 1, 90, 90, 191, 27, 6, 6, 3, 9, 3, 9, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
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: REAL300025051448 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(Cl)=CC=C2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [75, 32, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 145, 191, 191, 191, 191, 201, 201, 201, 192, 201, 201, 201, 191, 191, 32, 32, 1, 75, 145, 145, 191, 201, 191, 201, 191, 191, 191, 191] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 762
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051448 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(Cl)=CC=C2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [55, 55, 55, 146, 157, 201, 201, 201, 201, 201, 15, 9, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 146, 146, 201, 55, 15, 15, 6, 1, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [33, 34, 35, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39])
total number of confs: 658
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051448 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051448
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051448/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051448
Building REAL300025051449
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051449'
/scratch/stefan/7786831/working/building/REAL300025051449 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051449

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051449/0 /scratch/stefan/7786831/working/building/REAL300025051449 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 316)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/316
`/scratch/stefan/7786831/working/3D/316' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)O1)

`REAL300025051449.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051449.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051449/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051449 none CC1=C(C)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 2, 2, 1, 1, 1, 6, 20, 20, 20, 48, 55, 122, 123, 123, 123, 123, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 6, 6, 20, 48, 48, 123, 1, 1, 1, 1, 8, 8, 8] 201
rigid atoms, others: [39, 8, 9, 42, 7, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 43, 44, 45])
total number of confs: 304
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051449 none CC1=C(C)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 8, 8, 23, 55, 55, 55, 108, 120, 200, 201, 201, 201, 201, 8, 8, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 23, 23, 55, 108, 108, 201, 8, 8, 8, 8, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 23, 24, 25] set([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, 41, 42, 43, 44, 45])
total number of confs: 621
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051449 none CC1=C(C)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 123, 123, 123, 123, 95, 46, 46, 28, 46, 13, 1, 1, 1, 1, 1, 1, 1, 123, 123, 201, 201, 201, 201, 201, 201, 201, 201, 201, 123, 95, 95, 46, 28, 28, 1, 123, 123, 123, 123, 201, 201, 201] 201
rigid atoms, others: [38, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 609
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051449 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051449
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051449/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051449
Building REAL300025051450
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051450'
/scratch/stefan/7786831/working/building/REAL300025051450 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051450

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051450/0 /scratch/stefan/7786831/working/building/REAL300025051450 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 317)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/317
`/scratch/stefan/7786831/working/3D/317' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1)

`REAL300025051450.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051450.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051450/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051450 none COC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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: [5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 20, 20, 20, 73, 85, 177, 177, 177, 177, 177, 1, 1, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 20, 73, 73, 177, 1, 1, 1, 1, 5] 201
rigid atoms, others: [38, 39, 8, 9, 10, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 42])
total number of confs: 438
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051450 none COC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 55, 55, 55, 141, 157, 201, 201, 201, 201, 201, 5, 5, 1, 1, 2, 2, 2, 1, 1, 5, 12, 12, 55, 141, 141, 201, 5, 5, 5, 5, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 24, 25, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 652
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051450 none COC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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, 177, 177, 177, 177, 136, 76, 76, 31, 76, 13, 1, 1, 1, 1, 1, 1, 1, 177, 177, 201, 201, 201, 201, 201, 201, 201, 177, 136, 136, 76, 31, 31, 1, 177, 177, 177, 177, 201] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 702
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051450 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051450
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051450/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051450
Building REAL300025051451
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051451'
/scratch/stefan/7786831/working/building/REAL300025051451 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051451

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051451/0 /scratch/stefan/7786831/working/building/REAL300025051451 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 318)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/318
`/scratch/stefan/7786831/working/3D/318' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(C)=C1)

`REAL300025051451.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051451.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051451/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051451 none CC1=NN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 9, 2, 2, 2, 1, 1, 1, 7, 20, 20, 20, 53, 58, 135, 135, 135, 135, 135, 1, 1, 13, 13, 13, 13, 13, 13, 9, 9, 2, 7, 7, 20, 53, 53, 135, 1, 1, 1, 1, 13, 13, 13, 13] 201
rigid atoms, others: [38, 7, 8, 9, 39, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 42, 43, 44, 45])
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: REAL300025051451 none CC1=NN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 4, 13, 13, 13, 13, 29, 55, 55, 55, 113, 119, 201, 201, 201, 201, 201, 13, 13, 1, 1, 1, 2, 2, 2, 4, 4, 13, 29, 29, 55, 113, 113, 201, 13, 13, 13, 13, 2, 2, 2, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 45, 23, 24, 25] set([5, 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, 41, 42, 43, 44])
total number of confs: 630
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051451 none CC1=NN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 187, 135, 135, 135, 135, 99, 51, 51, 29, 51, 13, 1, 1, 1, 1, 1, 1, 1, 135, 135, 201, 201, 201, 201, 201, 201, 187, 187, 135, 99, 99, 51, 29, 29, 1, 135, 135, 135, 135, 201, 201, 201, 201] 201
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 815
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051451 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051451
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051451/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051451
Building REAL300025051452
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051452'
/scratch/stefan/7786831/working/building/REAL300025051452 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051452

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051452/0 /scratch/stefan/7786831/working/building/REAL300025051452 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 319)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/319
`/scratch/stefan/7786831/working/3D/319' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1)

`REAL300025051452.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051452.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051452/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051452 none COCC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 12, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 4, 6, 6, 6, 20, 37, 106, 106, 106, 106, 106, 1, 1, 4, 22, 22, 22, 12, 12, 4, 4, 2, 4, 4, 6, 20, 20, 106, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 261
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051452 none COCC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 8, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 9, 9, 9, 23, 40, 108, 108, 108, 108, 108, 4, 4, 1, 20, 20, 20, 8, 8, 1, 1, 4, 7, 7, 9, 23, 23, 108, 4, 4, 4, 4] 201
rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 25, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 267
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051452 none COCC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 108, 108, 108, 108, 106, 106, 106, 106, 85, 51, 51, 25, 51, 13, 1, 1, 1, 1, 1, 1, 1, 106, 106, 108, 201, 201, 201, 201, 201, 108, 108, 106, 85, 85, 51, 25, 25, 1, 106, 106, 106, 106] 201
rigid atoms, others: [39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 893
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051452 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051452
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051452/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051452
Building REAL300025051453
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051453'
/scratch/stefan/7786831/working/building/REAL300025051453 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051453

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051453/0 /scratch/stefan/7786831/working/building/REAL300025051453 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 320)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/320
`/scratch/stefan/7786831/working/3D/320' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(Cl)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051453.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051453.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051453/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051453 none CN1C=C(Cl)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 5, 23, 23, 23, 97, 116, 184, 184, 184, 184, 184, 1, 1, 4, 4, 4, 4, 4, 2, 5, 5, 23, 97, 97, 184, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 497
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051453 none CN1C=C(Cl)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 55, 55, 55, 146, 161, 201, 201, 201, 201, 201, 4, 4, 2, 2, 2, 1, 1, 4, 11, 11, 55, 146, 146, 201, 4, 4, 4, 4] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 639
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051453 none CN1C=C(Cl)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 184, 184, 184, 184, 150, 74, 74, 32, 74, 13, 1, 1, 1, 1, 1, 1, 1, 184, 184, 201, 201, 201, 201, 201, 184, 150, 150, 74, 32, 32, 1, 184, 184, 184, 184] 201
rigid atoms, others: [36, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 722
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051453 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051453
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051453/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051453
Building REAL300025051454
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051454'
/scratch/stefan/7786831/working/building/REAL300025051454 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051454

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051454/0 /scratch/stefan/7786831/working/building/REAL300025051454 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 321)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/321
`/scratch/stefan/7786831/working/3D/321' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)=CC1C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1(C)C)

`REAL300025051454.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051454.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051454/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051454 none CC(C)=CC1C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 2, 2, 2, 1, 1, 1, 7, 24, 24, 24, 73, 94, 175, 175, 175, 175, 175, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 3, 3, 2, 7, 7, 24, 73, 73, 175, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3] 201
rigid atoms, others: [8, 9, 10, 43, 44, 45, 46, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 47, 48, 49, 50, 51, 52])
total number of confs: 457
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051454 none CC(C)=CC1C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 3, 11, 33, 33, 33, 87, 109, 188, 188, 188, 188, 188, 3, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 1, 1, 3, 11, 11, 33, 87, 87, 188, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2] 201
rigid atoms, others: [34, 3, 4, 5, 6, 35, 24, 25, 26] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 530
number of broken/clashed sets: 42
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051454 none CC(C)=CC1C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 188, 175, 175, 175, 175, 137, 66, 66, 29, 66, 13, 1, 1, 1, 1, 1, 1, 1, 175, 175, 188, 188, 188, 201, 201, 201, 201, 201, 201, 201, 188, 188, 175, 137, 137, 66, 29, 29, 1, 175, 175, 175, 175, 188, 188, 188, 188, 188, 188] 201
rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 767
number of broken/clashed sets: 42
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051454 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051454
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051454/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051454
Building REAL300025051455
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051455'
/scratch/stefan/7786831/working/building/REAL300025051455 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051455

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051455/0 /scratch/stefan/7786831/working/building/REAL300025051455 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 322)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/322
`/scratch/stefan/7786831/working/3D/322' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1)

`REAL300025051455.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051455.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051455/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051455 none CC1=CC=C(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 11, 11, 9, 2, 2, 2, 1, 1, 1, 7, 14, 14, 14, 34, 54, 136, 136, 136, 136, 136, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9, 2, 7, 7, 14, 34, 34, 136, 1, 1, 1, 1, 11, 11] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 46, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48])
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: REAL300025051455 none CC1=CC=C(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 6, 19, 19, 19, 19, 41, 64, 64, 64, 112, 142, 201, 201, 201, 201, 201, 19, 19, 1, 1, 2, 2, 2, 1, 1, 3, 3, 6, 6, 19, 41, 41, 64, 112, 112, 201, 19, 19, 19, 19, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 47, 48, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 657
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051455 none CC1=CC=C(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 136, 136, 136, 136, 101, 63, 63, 30, 63, 13, 1, 1, 1, 1, 1, 1, 1, 136, 136, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 136, 101, 101, 63, 30, 30, 1, 136, 136, 136, 136, 201, 201] 201
rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48])
total number of confs: 843
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051455 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051455
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051455/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051455
Building REAL300025051456
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051456'
/scratch/stefan/7786831/working/building/REAL300025051456 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051456

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051456/0 /scratch/stefan/7786831/working/building/REAL300025051456 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 323)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/323
`/scratch/stefan/7786831/working/3D/323' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=NC=CN3C=C2)CC1)

`REAL300025051456.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051456.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051456/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051456 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=NC=CN3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 21, 21, 68, 78, 143, 143, 143, 143, 143, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 68, 68, 143, 21, 5, 5, 3, 9, 9, 9, 9, 9, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
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: REAL300025051456 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=NC=CN3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [72, 35, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 113, 143, 143, 143, 143, 201, 201, 201, 201, 201, 201, 201, 201, 143, 143, 35, 35, 1, 72, 113, 113, 143, 201, 201, 201, 201, 201, 143, 143, 143, 143] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 614
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051456 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=NC=CN3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [59, 59, 59, 140, 152, 201, 201, 201, 201, 201, 16, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 140, 140, 201, 59, 16, 16, 5, 1, 1, 1, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42])
total number of confs: 661
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051456 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051456
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051456/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051456
Building REAL300025051457
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051457'
/scratch/stefan/7786831/working/building/REAL300025051457 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051457

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051457/0 /scratch/stefan/7786831/working/building/REAL300025051457 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 324)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/324
`/scratch/stefan/7786831/working/3D/324' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=NC=CN32)CC1)

`REAL300025051457.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051457.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051457/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051457 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=NC=CN32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 19, 64, 77, 149, 149, 149, 149, 149, 5, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 64, 64, 149, 19, 5, 5, 3, 15, 15, 15, 15, 15, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 384
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051457 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=NC=CN32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [66, 29, 12, 1, 1, 1, 1, 1, 1, 1, 66, 66, 121, 149, 149, 149, 149, 201, 201, 201, 201, 201, 201, 201, 201, 149, 149, 29, 29, 1, 66, 121, 121, 149, 201, 201, 201, 201, 201, 149, 149, 149, 149] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 643
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051457 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=NC=CN32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [74, 74, 74, 148, 162, 201, 201, 201, 201, 201, 23, 15, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 148, 148, 201, 74, 23, 23, 9, 1, 1, 1, 1, 1, 15, 15, 15, 15] 201
rigid atoms, others: [34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42])
total number of confs: 680
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051457 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051457
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051457/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051457
Building REAL300025051458
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051458'
/scratch/stefan/7786831/working/building/REAL300025051458 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051458

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051458/0 /scratch/stefan/7786831/working/building/REAL300025051458 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 325)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/325
`/scratch/stefan/7786831/working/3D/325' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3NC=CC3=N2)CC1)

`REAL300025051458.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051458.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051458/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051458 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3NC=CC3=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 32, 32, 98, 107, 199, 199, 199, 199, 199, 7, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 98, 98, 199, 32, 7, 7, 3, 7, 7, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
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: REAL300025051458 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3NC=CC3=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 31, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 149, 199, 199, 199, 199, 201, 201, 201, 201, 201, 201, 201, 201, 199, 199, 31, 31, 1, 62, 149, 149, 199, 201, 201, 201, 201, 201, 199, 199, 199, 199] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 763
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051458 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3NC=CC3=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [51, 51, 51, 127, 134, 201, 201, 201, 201, 201, 12, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 127, 127, 201, 51, 12, 12, 4, 1, 1, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42])
total number of confs: 607
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051458 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051458/1 /scratch/stefan/7786831/working/building/REAL300025051458 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 326)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/326
`/scratch/stefan/7786831/working/3D/326' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3N=CC=C3N2)CC1)

`REAL300025051458.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051458.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051458/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051458 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3N=CC=C3N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 12, 28, 32, 46, 46, 46, 46, 46, 4, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 28, 28, 46, 12, 4, 4, 3, 14, 14, 14, 14, 14, 1, 1, 1, 1] 56
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 161
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051458 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3N=CC=C3N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [34, 20, 12, 1, 1, 1, 1, 1, 1, 1, 34, 34, 41, 46, 46, 46, 46, 56, 56, 56, 56, 56, 56, 56, 56, 46, 46, 20, 20, 1, 34, 41, 41, 46, 56, 56, 56, 56, 56, 46, 46, 46, 46] 56
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 188
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051458 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3N=CC=C3N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [32, 32, 32, 48, 50, 56, 56, 56, 56, 56, 18, 14, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 48, 48, 56, 32, 18, 18, 9, 1, 1, 1, 1, 1, 14, 14, 14, 14] 56
rigid atoms, others: [34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42])
total number of confs: 212
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051458 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051458
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051458/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051458/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051458
Building REAL300025051459
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051459'
/scratch/stefan/7786831/working/building/REAL300025051459 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051459

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051459/0 /scratch/stefan/7786831/working/building/REAL300025051459 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 327)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/327
`/scratch/stefan/7786831/working/3D/327' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN3N=NN=C3C=C2)CC1)

`REAL300025051459.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051459.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051459/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051459 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN3N=NN=C3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 8, 8, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 65, 77, 116, 116, 116, 116, 116, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 65, 65, 116, 24, 5, 5, 3, 9, 9, 9, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 341
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051459 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN3N=NN=C3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 8, 8, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [60, 28, 13, 1, 1, 1, 1, 1, 1, 1, 60, 60, 93, 116, 116, 116, 116, 201, 201, 201, 201, 201, 201, 201, 201, 116, 116, 28, 28, 1, 60, 93, 93, 116, 201, 201, 201, 116, 116, 116, 116] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 565
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051459 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN3N=NN=C3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 8, 8, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [70, 70, 70, 155, 170, 201, 201, 201, 201, 201, 16, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 155, 155, 201, 70, 16, 16, 5, 1, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [34, 35, 36, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40])
total number of confs: 682
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051459 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051459
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051459/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051459
Building REAL300025051460
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051460'
/scratch/stefan/7786831/working/building/REAL300025051460 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051460

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051460/0 /scratch/stefan/7786831/working/building/REAL300025051460 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 328)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/328
`/scratch/stefan/7786831/working/3D/328' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C)C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051460.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051460.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051460/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051460 none CC1=NN(C)C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 13, 13, 10, 2, 2, 2, 1, 1, 1, 6, 15, 15, 15, 42, 59, 130, 130, 130, 130, 130, 1, 1, 13, 13, 13, 13, 13, 13, 13, 10, 10, 2, 6, 6, 15, 42, 42, 130, 1, 1, 1, 1, 13] 201
rigid atoms, others: [43, 9, 10, 11, 44, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45])
total number of confs: 335
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051460 none CC1=NN(C)C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 13, 13, 13, 13, 29, 45, 45, 45, 89, 115, 201, 201, 201, 201, 201, 13, 13, 1, 2, 2, 2, 2, 2, 2, 4, 4, 13, 29, 29, 45, 89, 89, 201, 13, 13, 13, 13, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 45, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 582
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051460 none CC1=NN(C)C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 199, 130, 130, 130, 130, 94, 50, 50, 26, 50, 12, 1, 1, 1, 1, 1, 1, 1, 130, 130, 201, 201, 201, 201, 201, 201, 201, 199, 199, 130, 94, 94, 50, 26, 26, 1, 130, 130, 130, 130, 201] 201
rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45])
total number of confs: 842
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051460 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051460
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051460/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051460
Building REAL300025051461
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051461'
/scratch/stefan/7786831/working/building/REAL300025051461 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051461

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051461/0 /scratch/stefan/7786831/working/building/REAL300025051461 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 329)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/329
`/scratch/stefan/7786831/working/3D/329' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=C(Cl)S2)CC1)

`REAL300025051461.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051461.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051461/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051461 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=C(Cl)S2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 16, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 30, 108, 120, 200, 200, 200, 200, 200, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 1, 1, 108, 108, 200, 30, 6, 6, 3, 7, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31])
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: REAL300025051461 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=C(Cl)S2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 16, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [58, 31, 13, 1, 1, 1, 1, 1, 1, 1, 58, 58, 140, 200, 200, 200, 200, 201, 201, 201, 201, 201, 200, 200, 31, 31, 1, 58, 140, 140, 200, 201, 200, 200, 200, 200] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 747
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051461 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=C(Cl)S2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 16, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [45, 45, 45, 126, 134, 201, 201, 201, 201, 201, 12, 7, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 126, 126, 201, 45, 12, 12, 5, 1, 7, 7, 7, 7] 201
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 597
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051461 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051461
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051461/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051461
Building REAL300025051462
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051462'
/scratch/stefan/7786831/working/building/REAL300025051462 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051462

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051462/0 /scratch/stefan/7786831/working/building/REAL300025051462 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 330)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/330
`/scratch/stefan/7786831/working/3D/330' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=C3C=CC=CN32)CC1)

`REAL300025051462.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051462.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051462/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051462 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=C3C=CC=CN32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 29, 87, 93, 199, 199, 199, 199, 199, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 87, 87, 199, 29, 6, 6, 3, 7, 7, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 512
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051462 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=C3C=CC=CN32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [51, 31, 13, 1, 1, 1, 1, 1, 1, 1, 51, 51, 128, 199, 199, 199, 199, 201, 201, 201, 201, 201, 201, 201, 201, 199, 199, 31, 31, 1, 51, 128, 128, 199, 201, 201, 201, 201, 201, 199, 199, 199, 199] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 739
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051462 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=C3C=CC=CN32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [52, 52, 52, 126, 129, 201, 201, 201, 201, 201, 12, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 126, 126, 201, 52, 12, 12, 4, 1, 1, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42])
total number of confs: 633
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051462 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051462
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051462/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051462
Building REAL300025051463
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051463'
/scratch/stefan/7786831/working/building/REAL300025051463 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051463

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051463/0 /scratch/stefan/7786831/working/building/REAL300025051463 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 331)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/331
`/scratch/stefan/7786831/working/3D/331' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCCCC3=NO2)CC1)

`REAL300025051463.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051463.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051463/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051463 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCCCC3=NO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 8, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 30, 94, 109, 200, 200, 200, 200, 200, 6, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 94, 94, 200, 30, 6, 6, 3, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 533
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051463 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCCCC3=NO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 8, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 13, 1, 1, 1, 1, 1, 1, 1, 57, 57, 133, 200, 200, 200, 200, 201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 32, 32, 1, 57, 133, 133, 200, 201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 200, 200] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45])
total number of confs: 734
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051463 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCCCC3=NO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 8, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [54, 54, 54, 130, 140, 201, 201, 201, 201, 201, 13, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 130, 130, 201, 54, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44, 45])
total number of confs: 622
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051463 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051463
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051463/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051463
Building REAL300025051464
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051464'
/scratch/stefan/7786831/working/building/REAL300025051464 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051464

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051464/0 /scratch/stefan/7786831/working/building/REAL300025051464 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 332)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/332
`/scratch/stefan/7786831/working/3D/332' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN3C=CN=C3N=C2)CC1)

`REAL300025051464.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051464.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051464/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051464 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN3C=CN=C3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
186  conformations in input
total number of sets (complete confs): 186
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 25, 71, 83, 123, 123, 123, 123, 123, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 71, 71, 123, 25, 5, 5, 3, 9, 9, 9, 9, 1, 1, 1, 1] 186
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
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: REAL300025051464 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN3C=CN=C3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
186  conformations in input
total number of sets (complete confs): 186
using faster count positions algorithm for large data
unique positions, atoms: [63, 29, 13, 1, 1, 1, 1, 1, 1, 1, 63, 63, 97, 123, 123, 123, 123, 186, 186, 186, 186, 186, 186, 186, 186, 123, 123, 29, 29, 1, 63, 97, 97, 123, 186, 186, 186, 186, 123, 123, 123, 123] 186
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 556
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051464 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN3C=CN=C3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
186  conformations in input
total number of sets (complete confs): 186
using faster count positions algorithm for large data
unique positions, atoms: [71, 71, 71, 145, 159, 186, 186, 186, 186, 186, 15, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 145, 145, 186, 71, 15, 15, 5, 1, 1, 1, 1, 9, 9, 9, 9] 186
rigid atoms, others: [34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 625
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051464 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051464
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051464/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051464
Building REAL300025051465
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051465'
/scratch/stefan/7786831/working/building/REAL300025051465 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051465

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051465/0 /scratch/stefan/7786831/working/building/REAL300025051465 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 333)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/333
`/scratch/stefan/7786831/working/3D/333' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=NOC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051465.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051465.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051465/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051465 none O=C(CCC1=NOC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 8, 12, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 9, 16, 22, 22, 22, 22, 1, 1, 1, 6, 11, 11, 11, 35, 56, 139, 139, 139, 139, 139, 1, 1, 9, 9, 16, 16, 22, 22, 2, 6, 6, 11, 35, 35, 139, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 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: REAL300025051465 none O=C(CCC1=NOC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 8, 12, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 9, 4, 1, 1, 1, 1, 1, 1, 22, 22, 22, 35, 52, 52, 52, 103, 131, 201, 201, 201, 201, 201, 22, 22, 9, 9, 4, 4, 1, 1, 22, 35, 35, 52, 103, 103, 201, 22, 22, 22, 22] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 29, 30] set([0, 1, 2, 9, 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])
total number of confs: 651
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051465 none O=C(CCC1=NOC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 8, 12, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [139, 139, 139, 187, 199, 201, 201, 201, 201, 139, 110, 62, 62, 27, 62, 13, 1, 1, 1, 1, 1, 1, 1, 139, 139, 187, 187, 199, 199, 201, 201, 139, 110, 110, 62, 27, 27, 1, 139, 139, 139, 139] 201
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41])
total number of confs: 854
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051465 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051465
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051465/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051465
Building REAL300025051466
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051466'
/scratch/stefan/7786831/working/building/REAL300025051466 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051466

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051466/0 /scratch/stefan/7786831/working/building/REAL300025051466 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 334)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/334
`/scratch/stefan/7786831/working/3D/334' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CN=CN=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051466.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051466.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051466/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051466 none O=C(CCC1=CN=CN=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 5, 1, 1, 8, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 9, 11, 11, 11, 11, 11, 11, 1, 1, 1, 7, 13, 13, 13, 36, 54, 140, 140, 140, 140, 140, 1, 1, 9, 9, 11, 11, 11, 11, 11, 2, 7, 7, 13, 36, 36, 140, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 10, 11, 12, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 336
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051466 none O=C(CCC1=CN=CN=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 5, 1, 1, 8, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 5, 3, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 33, 48, 48, 48, 104, 134, 201, 201, 201, 201, 201, 18, 18, 5, 5, 3, 3, 1, 1, 1, 18, 33, 33, 48, 104, 104, 201, 18, 18, 18, 18] 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, 41, 42, 43])
total number of confs: 622
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051466 none O=C(CCC1=CN=CN=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 5, 1, 1, 8, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [140, 140, 140, 200, 201, 201, 201, 201, 201, 201, 140, 112, 58, 58, 27, 58, 12, 1, 1, 1, 1, 1, 1, 1, 140, 140, 200, 200, 201, 201, 201, 201, 201, 140, 112, 112, 58, 27, 27, 1, 140, 140, 140, 140] 201
rigid atoms, others: [39, 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, 40, 41, 42, 43])
total number of confs: 858
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051466 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051466
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051466/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051466
Building REAL300025051467
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051467'
/scratch/stefan/7786831/working/building/REAL300025051467 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051467

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051467/0 /scratch/stefan/7786831/working/building/REAL300025051467 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 335)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/335
`/scratch/stefan/7786831/working/3D/335' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=COC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC1=O)

`REAL300025051467.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051467.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051467/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051467 none COC1=COC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 6, 21, 21, 21, 65, 75, 198, 199, 199, 199, 199, 1, 1, 4, 4, 4, 6, 6, 6, 4, 2, 6, 6, 21, 65, 65, 199, 1, 1, 1, 1, 4] 201
rigid atoms, others: [38, 39, 8, 9, 10, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 42])
total number of confs: 450
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051467 none COC1=COC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 4, 4, 11, 26, 26, 26, 74, 84, 200, 201, 201, 201, 201, 4, 4, 1, 1, 1, 3, 3, 3, 1, 4, 11, 11, 26, 74, 74, 201, 4, 4, 4, 4, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 42, 24, 25, 26, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 478
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051467 none COC1=COC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 199, 199, 199, 199, 131, 51, 51, 29, 51, 13, 1, 1, 1, 1, 1, 1, 1, 199, 199, 201, 201, 201, 201, 201, 201, 201, 199, 131, 131, 51, 29, 29, 1, 199, 199, 199, 199, 201] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 760
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051467 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051467
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051467/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051467
Building REAL300025051468
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051468'
/scratch/stefan/7786831/working/building/REAL300025051468 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051468

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051468/0 /scratch/stefan/7786831/working/building/REAL300025051468 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 336)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/336
`/scratch/stefan/7786831/working/3D/336' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC1=O)

`REAL300025051468.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051468.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051468/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051468 none COC1=CNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 11, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 9, 9, 2, 2, 2, 1, 1, 1, 4, 9, 9, 9, 32, 49, 145, 145, 145, 145, 145, 1, 1, 9, 9, 9, 16, 16, 16, 9, 9, 2, 4, 4, 9, 32, 32, 145, 1, 1, 1, 1, 9] 201
rigid atoms, others: [39, 8, 9, 10, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 43])
total number of confs: 312
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051468 none COC1=CNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 11, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 15, 28, 28, 28, 70, 92, 201, 201, 201, 201, 201, 9, 9, 1, 1, 1, 4, 4, 4, 1, 1, 9, 15, 15, 28, 70, 70, 201, 9, 9, 9, 9, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 43, 24, 25, 26, 30, 31] set([0, 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])
total number of confs: 503
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051468 none COC1=CNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 11, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 145, 145, 145, 145, 112, 66, 66, 31, 66, 13, 1, 1, 1, 1, 1, 1, 1, 145, 145, 201, 201, 201, 201, 201, 201, 201, 201, 145, 112, 112, 66, 31, 31, 1, 145, 145, 145, 145, 201] 201
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42, 43])
total number of confs: 679
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051468 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051468
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051468/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051468
Building REAL300025051469
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051469'
/scratch/stefan/7786831/working/building/REAL300025051469 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051469

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051469/0 /scratch/stefan/7786831/working/building/REAL300025051469 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 337)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/337
`/scratch/stefan/7786831/working/3D/337' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(Cl)=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051469.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051469.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051469/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051469 none CC1=CC(Cl)=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 19, 19, 19, 51, 62, 102, 102, 102, 102, 102, 1, 1, 5, 5, 5, 5, 5, 5, 2, 4, 4, 19, 51, 51, 102, 1, 1, 1, 1, 5] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42])
total number of confs: 285
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051469 none CC1=CC(Cl)=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 65, 65, 65, 134, 155, 201, 201, 201, 201, 201, 5, 5, 1, 2, 2, 2, 1, 1, 5, 13, 13, 65, 134, 134, 201, 5, 5, 5, 5, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 42, 25, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 640
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051469 none CC1=CC(Cl)=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 102, 102, 102, 102, 84, 56, 56, 25, 56, 13, 1, 1, 1, 1, 1, 1, 1, 102, 102, 201, 201, 201, 201, 201, 201, 102, 84, 84, 56, 25, 25, 1, 102, 102, 102, 102, 201] 201
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 530
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051469 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051469
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051469/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051469
Building REAL300025051470
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051470'
/scratch/stefan/7786831/working/building/REAL300025051470 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051470

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051470/0 /scratch/stefan/7786831/working/building/REAL300025051470 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 338)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/338
`/scratch/stefan/7786831/working/3D/338' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN3C=[NH+]C=C3C=C2)CC1)

`REAL300025051470.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051470.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051470/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051470 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN3C=[NH+]C=C3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [7, 7, 7, 10, 10, 11, 11, 11, 11, 11, 5, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 10, 10, 11, 7, 5, 5, 3, 4, 4, 4, 4, 4, 1, 1, 1, 1] 11
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
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: REAL300025051470 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN3C=[NH+]C=C3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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, 10, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 11
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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])
total number of confs: 34
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051470 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN3C=[NH+]C=C3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [7, 7, 7, 10, 10, 11, 11, 11, 11, 11, 6, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 11, 7, 6, 6, 4, 1, 1, 1, 1, 1, 4, 4, 4, 4] 11
rigid atoms, others: [35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43])
total number of confs: 42
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051470 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051470/1 /scratch/stefan/7786831/working/building/REAL300025051470 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 339)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/339
`/scratch/stefan/7786831/working/3D/339' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN3C=NC=C3C=C2)CC1)

`REAL300025051470.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051470.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051470/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051470 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN3C=NC=C3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 67, 78, 130, 130, 130, 130, 130, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 67, 67, 130, 22, 5, 5, 3, 9, 9, 9, 9, 9, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
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: REAL300025051470 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN3C=NC=C3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [63, 29, 13, 1, 1, 1, 1, 1, 1, 1, 63, 63, 105, 130, 130, 130, 130, 201, 201, 201, 201, 201, 201, 201, 201, 130, 130, 29, 29, 1, 63, 105, 105, 130, 201, 201, 201, 201, 201, 130, 130, 130, 130] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 600
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051470 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN3C=NC=C3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [62, 62, 62, 156, 169, 201, 201, 201, 201, 201, 16, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 156, 156, 201, 62, 16, 16, 5, 1, 1, 1, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 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
/scratch/stefan/7786831/working/building/REAL300025051470 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051470
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051470/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051470/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051470
Building REAL300025051471
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051471'
/scratch/stefan/7786831/working/building/REAL300025051471 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051471

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051471/0 /scratch/stefan/7786831/working/building/REAL300025051471 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 340)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/340
`/scratch/stefan/7786831/working/3D/340' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051471.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051471.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051471/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051471 none CCC1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 17, 17, 17, 43, 53, 104, 104, 104, 104, 104, 1, 1, 5, 9, 9, 9, 9, 9, 5, 5, 2, 4, 4, 17, 43, 43, 104, 1, 1, 1, 1, 5] 201
rigid atoms, others: [43, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44])
total number of confs: 280
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051471 none CCC1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 5, 5, 5, 5, 9, 29, 29, 29, 62, 75, 125, 125, 125, 125, 125, 5, 5, 1, 3, 3, 3, 2, 2, 1, 1, 5, 9, 9, 29, 62, 62, 125, 5, 5, 5, 5, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 44, 25, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 355
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051471 none CCC1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 125, 125, 125, 125, 125, 104, 104, 104, 104, 91, 62, 62, 29, 62, 13, 1, 1, 1, 1, 1, 1, 1, 104, 104, 125, 201, 201, 201, 201, 201, 125, 125, 104, 91, 91, 62, 29, 29, 1, 104, 104, 104, 104, 125] 201
rigid atoms, others: [39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44])
total number of confs: 881
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051471 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051471
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051471/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051471
Building REAL300025051472
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051472'
/scratch/stefan/7786831/working/building/REAL300025051472 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051472

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051472/0 /scratch/stefan/7786831/working/building/REAL300025051472 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 341)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/341
`/scratch/stefan/7786831/working/3D/341' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CSC(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1)

`REAL300025051472.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051472.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051472/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051472 none CC1=CSC(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 14, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 17, 17, 15, 9, 2, 2, 2, 1, 1, 1, 6, 10, 10, 10, 36, 63, 140, 140, 140, 140, 140, 1, 1, 17, 17, 17, 17, 17, 15, 15, 9, 9, 2, 6, 6, 10, 36, 36, 140, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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: REAL300025051472 none CC1=CSC(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 14, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 4, 7, 17, 17, 17, 17, 25, 35, 35, 35, 85, 127, 201, 201, 201, 201, 201, 17, 17, 1, 2, 2, 2, 1, 4, 4, 7, 7, 17, 25, 25, 35, 85, 85, 201, 17, 17, 17, 17] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 29] set([6, 7, 8, 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: 556
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051472 none CC1=CSC(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 14, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 200, 140, 140, 140, 140, 126, 70, 70, 29, 70, 13, 1, 1, 1, 1, 1, 1, 1, 140, 140, 201, 201, 201, 201, 201, 201, 201, 200, 200, 140, 126, 126, 70, 29, 29, 1, 140, 140, 140, 140] 201
rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 836
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051472 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051472
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051472/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051472
Building REAL300025051473
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051473'
/scratch/stefan/7786831/working/building/REAL300025051473 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051473

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051473/0 /scratch/stefan/7786831/working/building/REAL300025051473 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 342)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/342
`/scratch/stefan/7786831/working/3D/342' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=CC=NC=C3N=C2)CC1)

`REAL300025051473.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051473.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051473/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051473 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=CC=NC=C3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
196  conformations in input
total number of sets (complete confs): 196
using faster count positions algorithm for large data
unique positions, atoms: [23, 23, 23, 73, 89, 134, 134, 134, 134, 134, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 73, 73, 134, 23, 5, 5, 3, 9, 9, 9, 9, 9, 1, 1, 1, 1] 196
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 383
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051473 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=CC=NC=C3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
196  conformations in input
total number of sets (complete confs): 196
using faster count positions algorithm for large data
unique positions, atoms: [70, 33, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 108, 134, 134, 134, 134, 196, 196, 196, 196, 196, 196, 196, 196, 196, 134, 134, 33, 33, 1, 70, 108, 108, 134, 196, 196, 196, 196, 196, 134, 134, 134, 134] 196
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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])
total number of confs: 593
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051473 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=CC=NC=C3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
196  conformations in input
total number of sets (complete confs): 196
using faster count positions algorithm for large data
unique positions, atoms: [68, 68, 68, 152, 170, 196, 196, 196, 196, 196, 16, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 152, 152, 196, 68, 16, 16, 5, 1, 1, 1, 1, 1, 9, 9, 9, 9] 196
rigid atoms, others: [35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43])
total number of confs: 666
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051473 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051473
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051473/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051473
Building REAL300025051474
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051474'
/scratch/stefan/7786831/working/building/REAL300025051474 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051474

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051474/0 /scratch/stefan/7786831/working/building/REAL300025051474 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 343)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/343
`/scratch/stefan/7786831/working/3D/343' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=C1C)

`REAL300025051474.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051474.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051474/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051474 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 28, 28, 28, 96, 114, 201, 201, 201, 201, 201, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 28, 96, 96, 201, 1, 1, 1, 1, 4, 4, 4] 201
rigid atoms, others: [38, 7, 8, 9, 39, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 42, 43, 44])
total number of confs: 550
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051474 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 4, 4, 13, 41, 41, 41, 108, 126, 201, 201, 201, 201, 201, 4, 4, 1, 1, 1, 2, 2, 2, 1, 1, 4, 13, 13, 41, 108, 108, 201, 4, 4, 4, 4, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 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])
total number of confs: 596
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051474 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 136, 61, 61, 29, 61, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 136, 136, 61, 29, 29, 1, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 745
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051474 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051474
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051474/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051474
Building REAL300025051475
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051475'
/scratch/stefan/7786831/working/building/REAL300025051475 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051475

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051475/0 /scratch/stefan/7786831/working/building/REAL300025051475 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 344)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/344
`/scratch/stefan/7786831/working/3D/344' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CN=CN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051475.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051475.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051475/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051475 none CC1=CN=CN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 23, 23, 23, 23, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 9, 18, 29, 98, 98, 98, 98, 98, 1, 1, 23, 23, 23, 23, 23, 9, 9, 2, 5, 5, 9, 18, 18, 98, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 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: REAL300025051475 none CC1=CN=CN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 23, 23, 23, 23, 33, 51, 51, 51, 99, 137, 201, 201, 201, 201, 201, 23, 23, 2, 2, 2, 1, 1, 6, 6, 23, 33, 33, 51, 99, 99, 201, 23, 23, 23, 23] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 633
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051475 none CC1=CN=CN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 172, 98, 98, 98, 98, 84, 46, 46, 28, 46, 13, 1, 1, 1, 1, 1, 1, 1, 98, 98, 201, 201, 201, 201, 201, 172, 172, 98, 84, 84, 46, 28, 28, 1, 98, 98, 98, 98] 201
rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 785
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051475 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051475/1 /scratch/stefan/7786831/working/building/REAL300025051475 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 345)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/345
`/scratch/stefan/7786831/working/3D/345' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C[NH+]=CN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051475.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051475.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051475/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051475 none CC1=C[NH+]=CN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.cat', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 6, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 15, 15, 15, 15, 7, 2, 2, 2, 1, 1, 1, 5, 10, 10, 10, 31, 37, 75, 75, 75, 75, 75, 1, 1, 15, 15, 15, 15, 15, 7, 7, 2, 5, 5, 10, 31, 31, 75, 1, 1, 1, 1] 96
rigid atoms, others: [43, 40, 41, 10, 11, 12, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 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: REAL300025051475 none CC1=C[NH+]=CN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.cat', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 6, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 5, 15, 15, 15, 15, 17, 29, 29, 29, 60, 67, 96, 96, 96, 96, 96, 15, 15, 2, 2, 2, 1, 1, 5, 5, 15, 17, 17, 29, 60, 60, 96, 15, 15, 15, 15] 96
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29, 30] set([8, 9, 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])
total number of confs: 311
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051475 none CC1=C[NH+]=CN1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.cat', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 6, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 93, 75, 75, 75, 75, 68, 56, 56, 29, 56, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 96, 96, 96, 96, 96, 93, 93, 75, 68, 68, 56, 29, 29, 1, 75, 75, 75, 75] 96
rigid atoms, others: [39, 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, 40, 41, 42, 43])
total number of confs: 369
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051475 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051475
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051475/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051475/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051475
Building REAL300025051476
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051476'
/scratch/stefan/7786831/working/building/REAL300025051476 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051476

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051476/0 /scratch/stefan/7786831/working/building/REAL300025051476 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 346)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/346
`/scratch/stefan/7786831/working/3D/346' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN(C3CCC3)N=N2)CC1)

`REAL300025051476.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051476.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051476/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051476 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN(C3CCC3)N=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 39, 43, 92, 92, 92, 92, 92, 4, 1, 1, 1, 3, 3, 3, 15, 15, 15, 64, 64, 64, 15, 15, 1, 1, 39, 39, 92, 16, 4, 4, 3, 15, 64, 64, 64, 64, 64, 64, 64, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 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: REAL300025051476 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN(C3CCC3)N=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [46, 27, 13, 1, 1, 1, 1, 1, 1, 1, 46, 46, 77, 92, 92, 92, 92, 129, 129, 129, 201, 201, 201, 129, 129, 92, 92, 27, 27, 1, 46, 77, 77, 92, 129, 201, 201, 201, 201, 201, 201, 201, 92, 92, 92, 92] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45])
total number of confs: 685
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051476 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN(C3CCC3)N=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [143, 143, 143, 183, 183, 201, 201, 201, 201, 201, 81, 64, 49, 49, 11, 49, 11, 11, 1, 1, 1, 1, 1, 11, 11, 64, 64, 183, 183, 201, 143, 81, 81, 49, 11, 1, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64] 201
rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45])
total number of confs: 721
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051476 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN(C3CCC3)N=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 90, 91, 129, 129, 129, 129, 129, 20, 15, 11, 11, 1, 11, 1, 1, 1, 1, 11, 11, 11, 1, 1, 15, 15, 90, 90, 129, 57, 20, 20, 11, 1, 11, 11, 11, 11, 11, 11, 11, 15, 15, 15, 15] 201
rigid atoms, others: [34, 14, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 432
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051476 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051476
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051476/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051476
Building REAL300025051477
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051477'
/scratch/stefan/7786831/working/building/REAL300025051477 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051477

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051477/0 /scratch/stefan/7786831/working/building/REAL300025051477 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 347)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/347
`/scratch/stefan/7786831/working/3D/347' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=NN2C2CCC2)CC1)

`REAL300025051477.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051477.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051477/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051477 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=NN2C2CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 16, 16, 51, 58, 103, 103, 103, 103, 103, 5, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 15, 15, 15, 1, 1, 51, 51, 103, 16, 5, 5, 3, 7, 7, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 311
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051477 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=NN2C2CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 30, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 90, 103, 103, 103, 103, 132, 132, 132, 132, 132, 201, 201, 201, 103, 103, 30, 30, 1, 61, 90, 90, 103, 132, 132, 201, 201, 201, 201, 201, 201, 201, 103, 103, 103, 103] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46])
total number of confs: 712
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051477 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=NN2C2CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [66, 66, 66, 157, 169, 201, 201, 201, 201, 201, 22, 15, 9, 9, 5, 9, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 15, 157, 157, 201, 66, 22, 22, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46])
total number of confs: 698
number of broken/clashed sets: 1
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051477 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=NN2C2CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [35, 35, 35, 92, 99, 132, 132, 132, 132, 132, 11, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 92, 92, 132, 35, 11, 11, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7] 201
rigid atoms, others: [34, 35, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 442
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051477 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051477
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051477/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051477
Building REAL300025051478
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051478'
/scratch/stefan/7786831/working/building/REAL300025051478 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051478

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051478/0 /scratch/stefan/7786831/working/building/REAL300025051478 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 348)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/348
`/scratch/stefan/7786831/working/3D/348' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=NN1C)

`REAL300025051478.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051478.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051478/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051478 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [199, 145, 145, 145, 145, 111, 63, 63, 28, 63, 13, 1, 1, 1, 1, 1, 1, 1, 145, 145, 199, 201, 201, 201, 201, 201, 199, 199, 199, 199, 145, 111, 111, 63, 28, 28, 1, 145, 145, 145, 145, 201, 201, 201, 201, 201] 201
rigid atoms, others: [36, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 824
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051478 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 2, 2, 2, 1, 1, 1, 6, 15, 15, 15, 40, 54, 145, 145, 145, 145, 145, 1, 1, 9, 15, 15, 15, 15, 15, 9, 9, 9, 9, 2, 6, 6, 15, 40, 40, 145, 1, 1, 1, 1, 15, 15, 15, 15, 15] 201
rigid atoms, others: [4, 5, 6, 39, 40, 18, 19, 38, 37] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45])
total number of confs: 349
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051478 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 15, 15, 15, 15, 29, 52, 52, 52, 104, 126, 201, 201, 201, 201, 201, 15, 15, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 15, 29, 29, 52, 104, 104, 201, 15, 15, 15, 15, 1, 1, 2, 2, 2] 201
rigid atoms, others: [1, 41, 42, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45])
total number of confs: 630
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051478 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051478
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051478/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051478
Building REAL300025051479
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051479'
/scratch/stefan/7786831/working/building/REAL300025051479 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051479

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051479/0 /scratch/stefan/7786831/working/building/REAL300025051479 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 349)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/349
`/scratch/stefan/7786831/working/3D/349' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=NSC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051479.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051479.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051479/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051479 none COC1=NSC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 14, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 7, 26, 26, 26, 66, 77, 147, 148, 148, 148, 148, 1, 1, 7, 7, 7, 7, 2, 7, 7, 26, 66, 66, 148, 1, 1, 1, 1, 7] 201
rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39])
total number of confs: 393
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051479 none COC1=NSC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 14, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 17, 52, 52, 52, 109, 122, 201, 201, 201, 201, 201, 7, 7, 1, 2, 2, 2, 7, 17, 17, 52, 109, 109, 201, 7, 7, 7, 7, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 578
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051479 none COC1=NSC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 14, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 148, 148, 148, 148, 96, 47, 47, 27, 47, 13, 1, 1, 1, 1, 1, 1, 1, 148, 148, 201, 201, 201, 201, 148, 96, 96, 47, 27, 27, 1, 148, 148, 148, 148, 201] 201
rigid atoms, others: [34, 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, 35, 36, 37, 38, 39])
total number of confs: 660
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051479 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051479
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051479/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051479
Building REAL300025051480
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051480'
/scratch/stefan/7786831/working/building/REAL300025051480 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051480

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051480/0 /scratch/stefan/7786831/working/building/REAL300025051480 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 350)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/350
`/scratch/stefan/7786831/working/3D/350' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN3CCCC3=N2)CC1)

`REAL300025051480.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051480.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051480/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051480 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN3CCCC3=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', '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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 30, 104, 113, 201, 201, 201, 201, 201, 6, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 1, 1, 104, 104, 201, 30, 6, 6, 3, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 553
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051480 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN3CCCC3=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', '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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 31, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 152, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 31, 31, 1, 61, 152, 152, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 748
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051480 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN3CCCC3=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', '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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [42, 42, 42, 122, 131, 201, 201, 201, 201, 201, 10, 6, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 122, 122, 201, 42, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43])
total number of confs: 600
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051480 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051480
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051480/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051480
Building REAL300025051481
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051481'
/scratch/stefan/7786831/working/building/REAL300025051481 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051481

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051481/0 /scratch/stefan/7786831/working/building/REAL300025051481 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 351)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/351
`/scratch/stefan/7786831/working/3D/351' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2=CC=NC=C2)CC1)

`REAL300025051481.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051481.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051481/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051481 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2=CC=NC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 53, 61, 145, 145, 145, 145, 145, 5, 1, 1, 1, 3, 3, 3, 19, 19, 19, 19, 19, 23, 23, 19, 23, 23, 1, 1, 53, 53, 145, 16, 5, 5, 3, 19, 19, 23, 23, 23, 23, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 390
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051481 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2=CC=NC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 124, 145, 145, 145, 145, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 145, 145, 32, 32, 1, 65, 124, 124, 145, 201, 201, 201, 201, 201, 201, 145, 145, 145, 145] 201
rigid atoms, others: [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, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 746
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051481 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2=CC=NC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 148, 154, 201, 201, 201, 201, 201, 31, 23, 15, 15, 3, 15, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 23, 23, 148, 148, 201, 78, 31, 31, 15, 3, 3, 1, 1, 1, 1, 23, 23, 23, 23] 201
rigid atoms, others: [38, 39, 40, 41, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45])
total number of confs: 675
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051481 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2=CC=NC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [74, 74, 74, 146, 153, 201, 201, 201, 201, 201, 27, 19, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 19, 19, 146, 146, 201, 74, 27, 27, 11, 1, 1, 3, 3, 3, 3, 19, 19, 19, 19] 201
rigid atoms, others: [36, 37, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 683
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051481 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051481
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051481/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051481
Building REAL300025051482
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051482'
/scratch/stefan/7786831/working/building/REAL300025051482 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051482

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051482/0 /scratch/stefan/7786831/working/building/REAL300025051482 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 352)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/352
`/scratch/stefan/7786831/working/3D/352' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1[C@H](C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC[N@@H+]1C)

`REAL300025051482.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051482.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051482/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051482 none C[C@@H]1[C@H](C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC[N@@H+]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 2, 5, 2, 2, 1, 1, 1, 6, 12, 12, 12, 21, 25, 35, 35, 35, 35, 35, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 2, 6, 6, 12, 21, 21, 35, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5] 35
rigid atoms, others: [38, 7, 8, 9, 39, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 123
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: REAL300025051482 none C[C@@H]1[C@H](C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC[N@@H+]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 5, 5, 5, 5, 8, 15, 15, 15, 23, 27, 35, 35, 35, 35, 35, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 15, 23, 23, 35, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2] 35
rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 43, 44, 45, 23, 24, 25, 26, 27] set([6, 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, 46, 47, 48])
total number of confs: 121
number of broken/clashed sets: 35
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051482 none C[C@@H]1[C@H](C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC[N@@H+]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 34, 31, 31, 18, 31, 9, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 34, 34, 31, 18, 18, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 35
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 118
number of broken/clashed sets: 35
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051482 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051482/1 /scratch/stefan/7786831/working/building/REAL300025051482 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 353)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/353
`/scratch/stefan/7786831/working/3D/353' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1[C@H](C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC[N@H+]1C)

`REAL300025051482.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051482.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051482/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051482 none C[C@@H]1[C@H](C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC[N@H+]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 2, 2, 2, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 5, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2] 5
rigid atoms, others: [38, 7, 8, 9, 39, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 18
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051482 none C[C@@H]1[C@H](C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC[N@H+]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 5, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2] 5
rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 43, 44, 45, 23, 24, 25, 26, 27] set([6, 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, 46, 47, 48])
total number of confs: 24
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051482 none C[C@@H]1[C@H](C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC[N@H+]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 4, 5, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 5
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 9
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051482 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051482
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051482/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051482/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051482
Building REAL300025051483
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051483'
/scratch/stefan/7786831/working/building/REAL300025051483 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051483

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051483/0 /scratch/stefan/7786831/working/building/REAL300025051483 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 354)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/354
`/scratch/stefan/7786831/working/3D/354' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C[C@@H]1C[C@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051483.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051483.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051483/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051483 none CC(C)(C)C[C@@H]1C[C@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 29, 29, 11, 11, 11, 11, 2, 11, 2, 2, 1, 1, 1, 4, 7, 7, 7, 21, 28, 80, 80, 80, 80, 80, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 11, 11, 2, 4, 4, 7, 21, 21, 80, 1, 1, 1, 1] 201
rigid atoms, others: [12, 13, 14, 48, 49, 50, 51, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 274
number of broken/clashed sets: 185
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051483 none CC(C)(C)C[C@@H]1C[C@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 26, 37, 37, 37, 70, 94, 177, 177, 177, 177, 177, 11, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 11, 26, 26, 37, 70, 70, 177, 11, 11, 11, 11] 201
rigid atoms, others: [4, 5, 6, 39, 8, 9, 10, 7, 40] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 494
number of broken/clashed sets: 185
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051483 none CC(C)(C)C[C@@H]1C[C@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 177, 177, 177, 177, 80, 177, 80, 80, 80, 73, 47, 47, 26, 47, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 177, 177, 80, 73, 73, 47, 26, 26, 1, 80, 80, 80, 80] 201
rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51])
total number of confs: 737
number of broken/clashed sets: 185
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051483 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051483
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051483/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051483
Building REAL300025051484
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051484'
/scratch/stefan/7786831/working/building/REAL300025051484 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051484

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051484/0 /scratch/stefan/7786831/working/building/REAL300025051484 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 355)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/355
`/scratch/stefan/7786831/working/3D/355' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C1=NN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1)

`REAL300025051484.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051484.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051484/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051484 none NC(=O)C1=NN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 15, 19, 15, 15, 8, 2, 2, 2, 1, 1, 1, 6, 23, 23, 23, 66, 78, 140, 140, 140, 140, 140, 1, 1, 15, 15, 19, 19, 8, 8, 2, 6, 6, 23, 66, 66, 140, 1, 1, 1, 1, 15] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42])
total number of confs: 427
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051484 none NC(=O)C1=NN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 6, 15, 15, 15, 15, 25, 55, 55, 55, 116, 133, 192, 192, 192, 192, 192, 15, 15, 1, 1, 3, 3, 6, 6, 15, 25, 25, 55, 116, 116, 192, 15, 15, 15, 15, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 42, 25, 26] set([0, 2, 7, 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: 618
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051484 none NC(=O)C1=NN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 192, 201, 192, 192, 184, 140, 140, 140, 140, 122, 69, 69, 37, 69, 13, 1, 1, 1, 1, 1, 1, 1, 140, 140, 192, 192, 201, 201, 184, 184, 140, 122, 122, 69, 37, 37, 1, 140, 140, 140, 140, 192] 201
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 826
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051484 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051484
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051484/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051484
Building REAL300025051485
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051485'
/scratch/stefan/7786831/working/building/REAL300025051485 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051485

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051485/0 /scratch/stefan/7786831/working/building/REAL300025051485 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 356)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/356
`/scratch/stefan/7786831/working/3D/356' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1[C@@H](C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC[N@@H+]1C)

`REAL300025051485.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051485.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051485/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051485 none CC[C@@H]1[C@@H](C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC[N@@H+]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 3, 3, 3, 2, 3, 2, 2, 1, 1, 1, 4, 5, 5, 5, 6, 6, 8, 8, 8, 8, 8, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 5, 6, 6, 8, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3] 8
rigid atoms, others: [43, 8, 9, 10, 23, 44, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 35
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: REAL300025051485 none CC[C@@H]1[C@@H](C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC[N@@H+]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 5, 5, 5, 6, 6, 8, 8, 8, 8, 8, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 4, 4, 5, 6, 6, 8, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2] 8
rigid atoms, others: [1, 2, 3, 4, 5, 6, 45, 46, 47, 48, 24, 25, 26, 27, 28] set([0, 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, 49, 50, 51])
total number of confs: 39
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051485 none CC[C@@H]1[C@@H](C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC[N@@H+]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 7, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 8
rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 22
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051485 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051485/1 /scratch/stefan/7786831/working/building/REAL300025051485 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 357)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/357
`/scratch/stefan/7786831/working/3D/357' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1[C@@H](C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC[N@H+]1C)

`REAL300025051485.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051485.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051485/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051485 none CC[C@@H]1[C@@H](C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC[N@H+]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [12, 6, 6, 6, 2, 6, 2, 2, 1, 1, 1, 6, 19, 19, 19, 38, 48, 102, 102, 102, 102, 102, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 2, 6, 6, 19, 38, 38, 102, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6] 110
rigid atoms, others: [43, 8, 9, 10, 23, 44, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 284
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: REAL300025051485 none CC[C@@H]1[C@@H](C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC[N@H+]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 15, 32, 32, 32, 54, 66, 110, 110, 110, 110, 110, 6, 6, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 6, 15, 15, 32, 54, 54, 110, 6, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2] 110
rigid atoms, others: [1, 2, 3, 4, 5, 6, 45, 46, 47, 48, 24, 25, 26, 27, 28] set([0, 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, 49, 50, 51])
total number of confs: 318
number of broken/clashed sets: 97
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051485 none CC[C@@H]1[C@@H](C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC[N@H+]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [110, 110, 110, 110, 102, 110, 102, 102, 102, 93, 78, 78, 27, 78, 11, 1, 1, 1, 1, 1, 1, 1, 102, 102, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 102, 93, 93, 78, 27, 27, 1, 102, 102, 102, 102, 110, 110, 110, 110, 110, 110, 110] 110
rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 375
number of broken/clashed sets: 97
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051485 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051485
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051485/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051485/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051485
Building REAL300025051486
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051486'
/scratch/stefan/7786831/working/building/REAL300025051486 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051486

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051486/0 /scratch/stefan/7786831/working/building/REAL300025051486 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 358)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/358
`/scratch/stefan/7786831/working/3D/358' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@@H]3C=C[C@H]2CC3)CC1)

`REAL300025051486.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051486.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051486/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051486 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@@H]3C=C[C@H]2CC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 5, 7, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 19, 72, 85, 169, 169, 169, 169, 169, 5, 1, 1, 1, 3, 3, 3, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 72, 72, 169, 19, 5, 5, 3, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1] 201
rigid atoms, others: [47, 44, 11, 12, 13, 46, 45, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 451
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: REAL300025051486 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@@H]3C=C[C@H]2CC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 5, 7, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [77, 32, 12, 1, 1, 1, 1, 1, 1, 1, 77, 77, 135, 169, 169, 169, 169, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 169, 169, 32, 32, 1, 77, 135, 135, 169, 201, 201, 201, 201, 201, 201, 201, 201, 169, 169, 169, 169] 201
rigid atoms, others: [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, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 748
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051486 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@@H]3C=C[C@H]2CC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 5, 7, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 61, 61, 138, 151, 201, 201, 201, 201, 201, 25, 16, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 138, 138, 201, 61, 25, 25, 10, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 14, 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, 15, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45, 46, 47])
total number of confs: 657
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051486 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051486
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051486/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051486
Building REAL300025051487
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051487'
/scratch/stefan/7786831/working/building/REAL300025051487 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051487

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051487/0 /scratch/stefan/7786831/working/building/REAL300025051487 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 359)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/359
`/scratch/stefan/7786831/working/3D/359' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN(CC)C(=O)CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051487.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051487.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051487/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051487 none CCN(CC)C(=O)CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [195, 155, 153, 155, 165, 142, 153, 142, 114, 114, 114, 114, 102, 66, 66, 26, 66, 12, 1, 1, 1, 1, 1, 1, 1, 114, 114, 195, 195, 195, 195, 195, 165, 165, 165, 165, 165, 142, 142, 142, 142, 114, 102, 102, 66, 26, 26, 1, 114, 114, 114, 114] 201
rigid atoms, others: [47, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51])
total number of confs: 955
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051487 none CCN(CC)C(=O)CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 9, 6, 9, 12, 4, 6, 3, 2, 2, 2, 1, 1, 1, 5, 9, 9, 9, 29, 45, 114, 114, 114, 114, 114, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 3, 3, 2, 5, 5, 9, 29, 29, 114, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 48, 49, 50, 51, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 303
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051487 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051487
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051487/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051487
Building REAL300025051488
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051488'
/scratch/stefan/7786831/working/building/REAL300025051488 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051488

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051488/0 /scratch/stefan/7786831/working/building/REAL300025051488 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 360)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/360
`/scratch/stefan/7786831/working/3D/360' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=CC=C1)

`REAL300025051488.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051488.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051488/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051488 none C=CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 117, 117, 117, 117, 109, 66, 66, 29, 66, 13, 1, 1, 1, 1, 1, 1, 1, 117, 117, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 117, 109, 109, 66, 29, 29, 1, 117, 117, 117, 117, 201, 201, 201, 201, 201] 201
rigid atoms, others: [37, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 825
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051488 none C=CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 10, 2, 2, 2, 1, 1, 1, 4, 9, 9, 9, 30, 48, 117, 117, 117, 117, 117, 1, 1, 10, 14, 14, 10, 14, 14, 15, 15, 15, 10, 2, 4, 4, 9, 30, 30, 117, 1, 1, 1, 1, 14, 14, 14, 14, 14] 201
rigid atoms, others: [5, 38, 7, 40, 41, 39, 19, 20, 6] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46])
total number of confs: 321
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051488 none C=CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 4, 1, 4, 14, 14, 14, 14, 28, 41, 41, 41, 90, 124, 201, 201, 201, 201, 201, 14, 14, 1, 1, 1, 1, 1, 1, 6, 6, 6, 4, 14, 28, 28, 41, 90, 90, 201, 14, 14, 14, 14, 1, 1, 1, 1, 1] 201
rigid atoms, others: [2, 42, 43, 44, 45, 46, 21, 22, 23, 24, 25, 26] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 596
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051488 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051488
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051488/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051488
Building REAL300025051489
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051489'
/scratch/stefan/7786831/working/building/REAL300025051489 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051489

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051489/0 /scratch/stefan/7786831/working/building/REAL300025051489 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 361)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/361
`/scratch/stefan/7786831/working/3D/361' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC=C1C(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051489.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051489.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051489/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051489 none CC1=CC=CC=C1C(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 5, 6, 6, 5, 2, 5, 2, 2, 1, 1, 1, 6, 18, 18, 18, 55, 64, 155, 156, 156, 156, 156, 1, 1, 6, 6, 6, 6, 5, 6, 6, 5, 5, 5, 5, 2, 6, 6, 18, 55, 55, 156, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 46, 45, 48, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
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: REAL300025051489 none CC1=CC=CC=C1C(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 20, 45, 45, 45, 109, 119, 201, 201, 201, 201, 201, 6, 6, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 4, 6, 20, 20, 45, 109, 109, 201, 6, 6, 6, 6] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 33, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 610
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051489 none CC1=CC=CC=C1C(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 156, 201, 156, 156, 156, 113, 49, 49, 28, 49, 13, 1, 1, 1, 1, 1, 1, 1, 156, 156, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 156, 113, 113, 49, 28, 28, 1, 156, 156, 156, 156] 201
rigid atoms, others: [44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48])
total number of confs: 830
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051489 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051489
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051489/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051489
Building REAL300025051490
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051490'
/scratch/stefan/7786831/working/building/REAL300025051490 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051490

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051490/0 /scratch/stefan/7786831/working/building/REAL300025051490 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 362)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/362
`/scratch/stefan/7786831/working/3D/362' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C(F)CC2=CC=CC=C2)CC1)

`REAL300025051490.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051490.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051490/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051490 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C(F)CC2=CC=CC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 15, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 43, 47, 94, 94, 94, 94, 94, 4, 1, 1, 1, 3, 3, 3, 23, 23, 46, 56, 56, 47, 56, 56, 1, 1, 43, 43, 94, 18, 4, 4, 3, 23, 46, 46, 56, 56, 46, 56, 56, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 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: REAL300025051490 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C(F)CC2=CC=CC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 15, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [52, 24, 13, 1, 1, 1, 1, 1, 1, 1, 52, 52, 84, 94, 94, 94, 94, 171, 171, 201, 201, 201, 201, 201, 201, 94, 94, 24, 24, 1, 52, 84, 84, 94, 171, 201, 201, 201, 201, 201, 201, 201, 94, 94, 94, 94] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45])
total number of confs: 888
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051490 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C(F)CC2=CC=CC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 15, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 193, 195, 201, 201, 201, 201, 201, 69, 56, 41, 41, 7, 41, 3, 7, 1, 1, 1, 1, 1, 1, 1, 56, 56, 193, 193, 201, 142, 69, 69, 41, 7, 3, 3, 1, 1, 1, 1, 1, 56, 56, 56, 56] 201
rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43, 44, 45])
total number of confs: 758
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051490 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051490
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051490/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051490
Building REAL300025051491
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051491'
/scratch/stefan/7786831/working/building/REAL300025051491 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051491

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051491/0 /scratch/stefan/7786831/working/building/REAL300025051491 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 363)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/363
`/scratch/stefan/7786831/working/3D/363' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(C)=N1)

`REAL300025051491.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051491.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051491/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051491 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 6, 20, 20, 20, 55, 68, 146, 147, 147, 147, 147, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 2, 6, 6, 20, 55, 55, 147, 1, 1, 1, 1, 9, 9, 9] 201
rigid atoms, others: [38, 7, 8, 9, 39, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 42, 43, 44])
total number of confs: 362
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051491 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 9, 9, 28, 59, 59, 59, 115, 131, 201, 201, 201, 201, 201, 9, 9, 1, 1, 1, 2, 2, 2, 1, 1, 9, 28, 28, 59, 115, 115, 201, 9, 9, 9, 9, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 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])
total number of confs: 619
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051491 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 147, 147, 147, 147, 111, 58, 58, 28, 58, 13, 1, 1, 1, 1, 1, 1, 1, 147, 147, 201, 201, 201, 201, 201, 201, 201, 201, 147, 111, 111, 58, 28, 28, 1, 147, 147, 147, 147, 201, 201, 201] 201
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 642
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051491 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051491
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051491/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051491
Building REAL300025051492
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051492'
/scratch/stefan/7786831/working/building/REAL300025051492 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051492

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051492/0 /scratch/stefan/7786831/working/building/REAL300025051492 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 364)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/364
`/scratch/stefan/7786831/working/3D/364' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)SC=C1)

`REAL300025051492.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051492.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051492/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051492 none CCC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)SC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 5, 5, 2, 2, 2, 1, 1, 1, 6, 16, 16, 16, 49, 61, 142, 142, 142, 142, 142, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 2, 6, 6, 16, 49, 49, 142, 1, 1, 1, 1, 5, 5] 201
rigid atoms, others: [37, 6, 7, 8, 39, 40, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 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, 36, 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051492 none CCC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)SC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 4, 4, 5, 5, 16, 33, 33, 33, 87, 98, 167, 167, 167, 167, 167, 5, 5, 1, 1, 1, 4, 4, 4, 4, 4, 5, 16, 16, 33, 87, 87, 167, 5, 5, 5, 5, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 41, 42, 22, 23, 24] set([0, 5, 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, 36, 37, 38, 39, 40])
total number of confs: 506
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051492 none CCC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)SC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 167, 167, 142, 142, 142, 142, 103, 51, 51, 25, 51, 13, 1, 1, 1, 1, 1, 1, 1, 142, 142, 167, 167, 167, 201, 201, 201, 201, 201, 142, 103, 103, 51, 25, 25, 1, 142, 142, 142, 142, 167, 167] 201
rigid atoms, others: [36, 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, 37, 38, 39, 40, 41, 42])
total number of confs: 795
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051492 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051492
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051492/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051492
Building REAL300025051493
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051493'
/scratch/stefan/7786831/working/building/REAL300025051493 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051493

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051493/0 /scratch/stefan/7786831/working/building/REAL300025051493 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 365)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/365
`/scratch/stefan/7786831/working/3D/365' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCC(C)[NH+]1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051493.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051493.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051493/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051493 none CC1CCC(C)[NH+]1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 4, 9, 9, 9, 16, 18, 28, 28, 28, 28, 28, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 9, 16, 16, 28, 1, 1, 1, 1] 28
rigid atoms, others: [11, 12, 13, 48, 49, 50, 51, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 94
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: REAL300025051493 none CC1CCC(C)[NH+]1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 2, 3, 3, 3, 3, 5, 9, 9, 9, 16, 18, 28, 28, 28, 28, 28, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 5, 5, 9, 16, 16, 28, 3, 3, 3, 3] 28
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 34, 35, 5, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 104
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051493 none CC1CCC(C)[NH+]1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 24, 24, 17, 24, 9, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 24, 17, 17, 1, 28, 28, 28, 28] 28
rigid atoms, others: [47, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51])
total number of confs: 101
number of broken/clashed sets: 28
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051493 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051493
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051493/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051493
Building REAL300025051494
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051494'
/scratch/stefan/7786831/working/building/REAL300025051494 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051494

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051494/0 /scratch/stefan/7786831/working/building/REAL300025051494 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 366)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/366
`/scratch/stefan/7786831/working/3D/366' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3=NN=CN3C2)CC1)

`REAL300025051494.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051494.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051494/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051494 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3=NN=CN3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 25, 81, 96, 171, 171, 171, 171, 171, 5, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 81, 81, 171, 25, 5, 5, 3, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 468
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051494 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3=NN=CN3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [76, 34, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 141, 171, 171, 171, 171, 201, 201, 201, 201, 201, 201, 201, 201, 171, 171, 34, 34, 1, 76, 141, 141, 171, 201, 201, 201, 201, 201, 201, 201, 201, 171, 171, 171, 171] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45])
total number of confs: 736
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051494 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3=NN=CN3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 146, 158, 201, 201, 201, 201, 201, 20, 13, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 146, 146, 201, 76, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44, 45])
total number of confs: 670
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051494 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051494
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051494/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051494
Building REAL300025051495
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051495'
/scratch/stefan/7786831/working/building/REAL300025051495 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051495

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051495/0 /scratch/stefan/7786831/working/building/REAL300025051495 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 367)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/367
`/scratch/stefan/7786831/working/3D/367' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCN1C=C(Cl)C=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051495.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051495.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051495/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051495 none O=C(CCN1C=C(Cl)C=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 16, 1, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 9, 12, 16, 16, 16, 16, 16, 1, 1, 1, 7, 21, 21, 21, 50, 66, 153, 153, 153, 153, 153, 1, 1, 9, 9, 12, 12, 16, 16, 2, 7, 7, 21, 50, 50, 153, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 10, 11, 12, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 408
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051495 none O=C(CCN1C=C(Cl)C=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 16, 1, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 9, 5, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 29, 53, 53, 53, 104, 123, 201, 201, 201, 201, 201, 16, 16, 9, 9, 5, 5, 1, 1, 16, 29, 29, 53, 104, 104, 201, 16, 16, 16, 16] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 639
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051495 none O=C(CCN1C=C(Cl)C=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 16, 1, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [153, 153, 153, 201, 201, 201, 201, 201, 201, 201, 153, 112, 49, 49, 27, 49, 12, 1, 1, 1, 1, 1, 1, 1, 153, 153, 201, 201, 201, 201, 201, 201, 153, 112, 112, 49, 27, 27, 1, 153, 153, 153, 153] 201
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42])
total number of confs: 816
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051495 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051495
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051495/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051495
Building REAL300025051496
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051496'
/scratch/stefan/7786831/working/building/REAL300025051496 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051496

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051496/0 /scratch/stefan/7786831/working/building/REAL300025051496 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 368)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/368
`/scratch/stefan/7786831/working/3D/368' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCCOC(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051496.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051496.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051496/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051496 none CCOCCOC(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 194, 172, 121, 77, 72, 77, 72, 72, 72, 67, 26, 26, 23, 26, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 201, 201, 201, 201, 201, 194, 194, 172, 172, 77, 77, 77, 77, 72, 67, 67, 26, 23, 23, 1, 72, 72, 72, 72] 201
rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49])
total number of confs: 800
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051496 none CCOCCOC(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [59, 53, 25, 14, 7, 3, 2, 3, 2, 2, 1, 1, 1, 4, 12, 12, 12, 28, 29, 72, 72, 72, 72, 72, 1, 1, 59, 59, 59, 59, 59, 25, 25, 14, 14, 3, 3, 3, 3, 2, 4, 4, 12, 28, 28, 72, 1, 1, 1, 1] 201
rigid atoms, others: [10, 11, 12, 46, 47, 48, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 351
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051496 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051496
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051496/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051496
Building REAL300025051497
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051497'
/scratch/stefan/7786831/working/building/REAL300025051497 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051497

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051497/0 /scratch/stefan/7786831/working/building/REAL300025051497 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 369)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/369
`/scratch/stefan/7786831/working/3D/369' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=CC3=CC=CC=C32)CC1)

`REAL300025051497.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051497.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051497/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051497 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=CC3=CC=CC=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 19, 49, 58, 123, 123, 123, 123, 123, 5, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 49, 49, 123, 19, 5, 5, 3, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 42, 11, 12, 13, 44, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 317
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051497 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=CC3=CC=CC=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [53, 29, 13, 1, 1, 1, 1, 1, 1, 1, 53, 53, 92, 123, 123, 123, 123, 201, 201, 201, 201, 201, 201, 201, 201, 201, 123, 123, 29, 29, 1, 53, 92, 92, 123, 201, 201, 201, 201, 201, 201, 123, 123, 123, 123] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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])
total number of confs: 578
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051497 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=CC3=CC=CC=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 122, 134, 201, 201, 201, 201, 201, 21, 15, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 122, 122, 201, 64, 21, 21, 8, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15] 201
rigid atoms, others: [35, 36, 37, 38, 39, 40, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44])
total number of confs: 624
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051497 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051497
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051497/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051497
Building REAL300025051498
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051498'
/scratch/stefan/7786831/working/building/REAL300025051498 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051498

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051498/0 /scratch/stefan/7786831/working/building/REAL300025051498 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 370)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/370
`/scratch/stefan/7786831/working/3D/370' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1)

`REAL300025051498.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051498.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051498/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051498 none CN1C=C(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 11, 8, 2, 2, 2, 1, 1, 1, 7, 12, 12, 12, 31, 45, 80, 80, 80, 80, 80, 1, 1, 13, 13, 13, 13, 13, 13, 11, 11, 8, 8, 2, 7, 7, 12, 31, 31, 80, 1, 1, 1, 1, 13] 87
rigid atoms, others: [43, 8, 9, 10, 23, 44, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 45])
total number of confs: 259
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051498 none CN1C=C(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 3, 6, 13, 13, 13, 13, 18, 22, 22, 22, 43, 56, 87, 87, 87, 87, 87, 13, 13, 1, 1, 2, 2, 2, 1, 3, 3, 6, 6, 13, 18, 18, 22, 43, 43, 87, 13, 13, 13, 13, 1] 87
rigid atoms, others: [0, 1, 2, 3, 4, 45, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 277
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051498 none CN1C=C(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 80, 80, 80, 80, 76, 60, 60, 29, 60, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 80, 76, 76, 60, 29, 29, 1, 80, 80, 80, 80, 87] 87
rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45])
total number of confs: 329
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051498 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051498
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051498/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051498
Building REAL300025051499
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051499'
/scratch/stefan/7786831/working/building/REAL300025051499 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051499

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051499/0 /scratch/stefan/7786831/working/building/REAL300025051499 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 371)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/371
`/scratch/stefan/7786831/working/3D/371' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC[NH+]1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051499.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051499.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051499/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051499 none O=C(CCC[NH+]1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [2, 2, 2, 7, 6, 8, 15, 15, 15, 15, 15, 1, 1, 1, 3, 5, 5, 5, 12, 18, 45, 45, 45, 45, 45, 1, 1, 7, 7, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 2, 3, 3, 5, 12, 12, 45, 1, 1, 1, 1] 47
rigid atoms, others: [11, 12, 13, 48, 49, 50, 51, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 162
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051499 none O=C(CCC[NH+]1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [15, 12, 6, 5, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 16, 16, 16, 28, 34, 47, 47, 47, 47, 47, 15, 15, 12, 12, 6, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 16, 28, 28, 47, 15, 15, 15, 15] 47
rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 39, 40, 36, 38, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 164
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051499 none O=C(CCC[NH+]1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [45, 45, 45, 47, 45, 47, 47, 47, 47, 47, 47, 45, 44, 35, 35, 24, 35, 12, 1, 1, 1, 1, 1, 1, 1, 45, 45, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 45, 44, 44, 35, 24, 24, 1, 45, 45, 45, 45] 47
rigid atoms, others: [47, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51])
total number of confs: 200
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051499 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051499
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051499/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051499
Building REAL300025051500
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051500'
/scratch/stefan/7786831/working/building/REAL300025051500 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051500

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051500/0 /scratch/stefan/7786831/working/building/REAL300025051500 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 372)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/372
`/scratch/stefan/7786831/working/3D/372' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1)

`REAL300025051500.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051500.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051500/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051500 none CC1=CC=C(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 29, 29, 15, 9, 2, 2, 2, 1, 1, 1, 4, 7, 7, 7, 25, 48, 120, 120, 120, 120, 120, 1, 1, 29, 29, 29, 29, 29, 29, 15, 15, 9, 9, 2, 4, 4, 7, 25, 25, 120, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
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: REAL300025051500 none CC1=CC=C(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 10, 28, 28, 29, 29, 39, 53, 53, 53, 108, 143, 201, 201, 201, 201, 201, 29, 29, 1, 2, 2, 2, 1, 1, 5, 5, 10, 10, 29, 39, 39, 53, 108, 108, 201, 29, 29, 29, 29] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 651
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051500 none CC1=CC=C(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 199, 195, 120, 120, 120, 120, 104, 69, 69, 30, 69, 13, 1, 1, 1, 1, 1, 1, 1, 120, 120, 201, 201, 201, 201, 201, 201, 199, 199, 195, 195, 120, 104, 104, 69, 30, 30, 1, 120, 120, 120, 120] 201
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 860
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051500 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051500
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051500/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051500
Building REAL300025051501
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051501'
/scratch/stefan/7786831/working/building/REAL300025051501 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051501

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051501/0 /scratch/stefan/7786831/working/building/REAL300025051501 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 373)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/373
`/scratch/stefan/7786831/working/3D/373' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=NC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CS1)

`REAL300025051501.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051501.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051501/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051501 none CCC1=NC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 1, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 7, 7, 2, 2, 2, 1, 1, 1, 4, 11, 11, 11, 32, 42, 89, 89, 89, 89, 89, 1, 1, 7, 7, 21, 21, 21, 21, 21, 7, 7, 2, 4, 4, 11, 32, 32, 89, 1, 1, 1, 1, 7] 201
rigid atoms, others: [8, 9, 10, 43, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 44])
total number of confs: 283
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051501 none CCC1=NC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 1, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 1, 1, 1, 1, 3, 7, 7, 7, 7, 13, 29, 29, 29, 58, 72, 124, 124, 124, 124, 124, 7, 7, 1, 1, 6, 6, 6, 6, 6, 3, 3, 7, 13, 13, 29, 58, 58, 124, 7, 7, 7, 7, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 44, 24, 25] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 362
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051501 none CCC1=NC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 1, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 124, 124, 124, 124, 89, 89, 89, 89, 78, 61, 61, 44, 61, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 124, 124, 201, 201, 201, 201, 201, 124, 124, 89, 78, 78, 61, 44, 44, 1, 89, 89, 89, 89, 124] 201
rigid atoms, others: [39, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44])
total number of confs: 978
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051501 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051501
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051501/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051501
Building REAL300025051502
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051502'
/scratch/stefan/7786831/working/building/REAL300025051502 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051502

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051502/0 /scratch/stefan/7786831/working/building/REAL300025051502 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 374)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/374
`/scratch/stefan/7786831/working/3D/374' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1)

`REAL300025051502.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051502.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051502/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051502 none CC1=CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 21, 21, 21, 12, 2, 2, 2, 1, 1, 1, 5, 9, 9, 9, 32, 52, 123, 123, 123, 123, 123, 1, 1, 21, 21, 21, 21, 21, 21, 12, 12, 2, 5, 5, 9, 32, 32, 123, 1, 1, 1, 1] 201
rigid atoms, others: [39, 8, 9, 10, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 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: REAL300025051502 none CC1=CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 21, 21, 21, 21, 38, 53, 53, 53, 96, 128, 201, 201, 201, 201, 201, 21, 21, 1, 2, 2, 2, 1, 1, 6, 6, 21, 38, 38, 53, 96, 96, 201, 21, 21, 21, 21] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 603
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051502 none CC1=CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 195, 123, 123, 123, 123, 113, 68, 68, 28, 68, 13, 1, 1, 1, 1, 1, 1, 1, 123, 123, 201, 201, 201, 201, 201, 201, 195, 195, 123, 113, 113, 68, 28, 28, 1, 123, 123, 123, 123] 201
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42])
total number of confs: 838
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051502 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051502
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051502/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051502
Building REAL300025051503
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051503'
/scratch/stefan/7786831/working/building/REAL300025051503 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051503

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051503/0 /scratch/stefan/7786831/working/building/REAL300025051503 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 375)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/375
`/scratch/stefan/7786831/working/3D/375' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CC[NH+]1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1)

`REAL300025051503.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051503.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051503/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051503 none C#CC[NH+]1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [11, 11, 6, 6, 6, 6, 6, 2, 2, 2, 1, 1, 1, 3, 5, 5, 5, 14, 16, 24, 24, 24, 24, 24, 1, 1, 6, 6, 11, 11, 11, 6, 6, 6, 6, 6, 2, 3, 3, 5, 14, 14, 24, 1, 1, 1, 1, 6, 6, 6, 6] 43
rigid atoms, others: [43, 44, 10, 11, 12, 45, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50])
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: REAL300025051503 none C#CC[NH+]1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 7, 11, 11, 11, 21, 23, 27, 27, 27, 27, 27, 6, 6, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 6, 7, 7, 11, 21, 21, 27, 6, 6, 6, 6, 1, 1, 1, 1] 43
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 47, 48, 49, 50, 35, 26, 27, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 105
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051503 none C#CC[NH+]1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [43, 43, 27, 27, 27, 27, 27, 24, 24, 24, 24, 24, 20, 20, 11, 20, 8, 1, 1, 1, 1, 1, 1, 1, 24, 24, 27, 27, 43, 43, 43, 27, 27, 27, 27, 27, 24, 24, 24, 20, 11, 11, 1, 24, 24, 24, 24, 27, 27, 27, 27] 43
rigid atoms, others: [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, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 184
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051503 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051503
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051503/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051503
Building REAL300025051504
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051504'
/scratch/stefan/7786831/working/building/REAL300025051504 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051504

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051504/0 /scratch/stefan/7786831/working/building/REAL300025051504 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 376)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/376
`/scratch/stefan/7786831/working/3D/376' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC[NH+]1CCCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051504.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051504.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051504/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051504 none O=C(CC[NH+]1CCCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [2, 2, 2, 6, 7, 10, 10, 10, 10, 10, 10, 1, 1, 1, 5, 8, 8, 8, 21, 22, 35, 35, 35, 35, 35, 1, 1, 6, 6, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 5, 5, 8, 21, 21, 35, 1, 1, 1, 1] 45
rigid atoms, others: [11, 12, 13, 48, 49, 50, 51, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 141
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051504 none O=C(CC[NH+]1CCCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [10, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 12, 20, 20, 20, 34, 36, 45, 45, 45, 45, 45, 10, 10, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 12, 12, 20, 34, 34, 45, 10, 10, 10, 10] 45
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 39, 40, 35, 36, 38, 37, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 167
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051504 none O=C(CC[NH+]1CCCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [35, 35, 35, 35, 35, 45, 45, 45, 45, 45, 45, 35, 33, 29, 29, 13, 29, 10, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 35, 33, 33, 29, 13, 13, 1, 35, 35, 35, 35] 45
rigid atoms, others: [47, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51])
total number of confs: 151
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051504 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051504
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051504/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051504
Building REAL300025051505
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051505'
/scratch/stefan/7786831/working/building/REAL300025051505 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051505

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051505/0 /scratch/stefan/7786831/working/building/REAL300025051505 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 377)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/377
`/scratch/stefan/7786831/working/3D/377' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CN(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=C1)

`REAL300025051505.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051505.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051505/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051505 none CC1=CN(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 12, 8, 2, 2, 2, 1, 1, 1, 7, 19, 19, 19, 59, 84, 168, 168, 168, 168, 168, 1, 1, 13, 13, 13, 13, 13, 13, 12, 12, 8, 8, 2, 7, 7, 19, 59, 59, 168, 1, 1, 1, 1, 13] 201
rigid atoms, others: [43, 8, 9, 10, 23, 44, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 45])
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051505 none CC1=CN(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 5, 8, 13, 13, 13, 13, 25, 47, 47, 47, 100, 125, 201, 201, 201, 201, 201, 13, 13, 1, 1, 2, 2, 2, 1, 5, 5, 8, 8, 13, 25, 25, 47, 100, 100, 201, 13, 13, 13, 13, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 45, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 610
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051505 none CC1=CN(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 200, 168, 168, 168, 168, 132, 66, 66, 28, 66, 12, 1, 1, 1, 1, 1, 1, 1, 168, 168, 201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 168, 132, 132, 66, 28, 28, 1, 168, 168, 168, 168, 201] 201
rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45])
total number of confs: 804
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051505 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051505
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051505/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051505
Building REAL300025051506
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051506'
/scratch/stefan/7786831/working/building/REAL300025051506 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051506

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051506/0 /scratch/stefan/7786831/working/building/REAL300025051506 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 378)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/378
`/scratch/stefan/7786831/working/3D/378' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCS(=O)(=O)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051506.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051506.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051506/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051506 none CCS(=O)(=O)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 14, 11, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 200, 201, 201, 158, 158, 158, 158, 133, 72, 72, 32, 72, 13, 1, 1, 1, 1, 1, 1, 1, 158, 158, 201, 201, 201, 201, 201, 200, 200, 158, 133, 133, 72, 32, 32, 1, 158, 158, 158, 158] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41])
total number of confs: 857
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051506 none CCS(=O)(=O)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 14, 11, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 13, 8, 13, 13, 2, 2, 2, 1, 1, 1, 6, 15, 15, 15, 42, 69, 157, 158, 158, 158, 158, 1, 1, 15, 15, 15, 15, 15, 8, 8, 2, 6, 6, 15, 42, 42, 158, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 8, 9, 10, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
total number of confs: 394
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051506 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051506
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051506/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051506
Building REAL300025051507
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051507'
/scratch/stefan/7786831/working/building/REAL300025051507 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051507

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051507/0 /scratch/stefan/7786831/working/building/REAL300025051507 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 379)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/379
`/scratch/stefan/7786831/working/3D/379' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)CN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=N1)

`REAL300025051507.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051507.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051507/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051507 none NC(=O)CN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=N1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 6, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 9, 20, 3, 3, 3, 2, 2, 2, 1, 1, 1, 4, 8, 8, 8, 28, 43, 128, 128, 128, 128, 128, 1, 1, 3, 3, 20, 20, 9, 9, 3, 2, 4, 4, 8, 28, 28, 128, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 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: REAL300025051507 none NC(=O)CN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=N1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 6, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 7, 16, 1, 1, 1, 1, 1, 2, 2, 3, 3, 6, 11, 11, 11, 33, 51, 138, 138, 138, 138, 138, 3, 3, 1, 1, 16, 16, 7, 7, 1, 3, 6, 6, 11, 33, 33, 138, 3, 3, 3, 3] 201
rigid atoms, others: [3, 4, 5, 6, 7, 25, 26, 31] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 342
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051507 none NC(=O)CN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=N1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 6, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 138, 138, 138, 128, 128, 128, 128, 103, 60, 60, 27, 60, 13, 1, 1, 1, 1, 1, 1, 1, 128, 128, 138, 138, 201, 201, 201, 201, 138, 128, 103, 103, 60, 27, 27, 1, 128, 128, 128, 128] 201
rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 855
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051507 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051507
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051507/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051507
Building REAL300025051508
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051508'
/scratch/stefan/7786831/working/building/REAL300025051508 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051508

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051508/0 /scratch/stefan/7786831/working/building/REAL300025051508 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 380)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/380
`/scratch/stefan/7786831/working/3D/380' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@H]2CCCO2)CC1)

`REAL300025051508.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051508.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051508/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051508 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@H]2CCCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 26, 77, 84, 183, 183, 183, 183, 183, 6, 1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 1, 1, 77, 77, 183, 26, 6, 6, 3, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 472
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051508 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@H]2CCCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 12, 1, 1, 1, 1, 1, 1, 1, 55, 55, 139, 183, 183, 183, 183, 201, 201, 201, 201, 201, 183, 183, 33, 33, 1, 55, 139, 139, 183, 201, 201, 201, 201, 201, 201, 183, 183, 183, 183] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 772
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051508 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@H]2CCCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 127, 132, 201, 201, 201, 201, 201, 19, 12, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 12, 127, 127, 201, 63, 19, 19, 8, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12] 201
rigid atoms, others: [32, 33, 34, 35, 36, 14, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40])
total number of confs: 635
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051508 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051508
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051508/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051508
Building REAL300025051509
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051509'
/scratch/stefan/7786831/working/building/REAL300025051509 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051509

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051509/0 /scratch/stefan/7786831/working/building/REAL300025051509 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 381)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/381
`/scratch/stefan/7786831/working/3D/381' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051509.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051509.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051509/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051509 none O=C(CCC(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 15, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [76, 76, 76, 168, 191, 201, 201, 76, 72, 45, 45, 24, 45, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 168, 168, 199, 199, 201, 76, 72, 72, 45, 24, 24, 1, 76, 76, 76, 76] 201
rigid atoms, others: [34, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 921
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051509 none O=C(CCC(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 15, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 10, 17, 41, 41, 1, 1, 1, 4, 14, 14, 14, 35, 37, 76, 76, 76, 76, 76, 1, 1, 10, 10, 22, 22, 37, 2, 4, 4, 14, 35, 35, 76, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 379
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051509 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051509
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051509/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051509
Building REAL300025051510
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051510'
/scratch/stefan/7786831/working/building/REAL300025051510 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051510

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051510/0 /scratch/stefan/7786831/working/building/REAL300025051510 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 382)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/382
`/scratch/stefan/7786831/working/3D/382' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC(=O)N1)

`REAL300025051510.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051510.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051510/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051510 none CCC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'H', '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, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 14, 14, 14, 38, 46, 95, 95, 95, 95, 95, 1, 1, 5, 5, 5, 5, 9, 9, 9, 9, 9, 5, 2, 4, 4, 14, 38, 38, 95, 1, 1, 1, 1, 5, 5] 201
rigid atoms, others: [7, 8, 9, 42, 43, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 44, 45])
total number of confs: 258
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051510 none CCC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'H', '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, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 5, 5, 11, 30, 30, 30, 64, 75, 130, 130, 130, 130, 130, 5, 5, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 5, 11, 11, 30, 64, 64, 130, 5, 5, 5, 5, 1, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 44, 45, 23, 24, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 365
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051510 none CCC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'H', '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, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 130, 130, 130, 95, 95, 95, 95, 82, 64, 64, 30, 64, 13, 1, 1, 1, 1, 1, 1, 1, 95, 95, 130, 130, 130, 130, 201, 201, 201, 201, 201, 130, 95, 82, 82, 64, 30, 30, 1, 95, 95, 95, 95, 130, 130] 201
rigid atoms, others: [39, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45])
total number of confs: 835
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051510 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051510
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051510/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051510
Building REAL300025051511
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051511'
/scratch/stefan/7786831/working/building/REAL300025051511 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051511

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051511/0 /scratch/stefan/7786831/working/building/REAL300025051511 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 383)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/383
`/scratch/stefan/7786831/working/3D/383' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=NOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051511.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051511.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051511/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051511 none CCOC1=NOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', '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, 8, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 6, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 6, 14, 14, 14, 51, 83, 182, 182, 182, 182, 182, 1, 1, 3, 12, 12, 12, 12, 12, 2, 6, 6, 14, 51, 51, 182, 1, 1, 1, 1, 3] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42])
total number of confs: 423
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051511 none CCOC1=NOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', '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, 8, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 4, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 8, 17, 17, 17, 56, 89, 183, 183, 183, 183, 183, 3, 3, 1, 10, 10, 10, 9, 9, 3, 8, 8, 17, 56, 56, 183, 3, 3, 3, 3, 1] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 42, 25] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 443
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051511 none CCOC1=NOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', '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, 8, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 200, 183, 183, 183, 183, 182, 182, 182, 182, 138, 72, 72, 31, 72, 13, 1, 1, 1, 1, 1, 1, 1, 182, 182, 183, 201, 201, 201, 201, 201, 182, 138, 138, 72, 31, 31, 1, 182, 182, 182, 182, 183] 201
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 754
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051511 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051511
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051511/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051511
Building REAL300025051512
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051512'
/scratch/stefan/7786831/working/building/REAL300025051512 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051512

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051512/0 /scratch/stefan/7786831/working/building/REAL300025051512 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 384)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/384
`/scratch/stefan/7786831/working/3D/384' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3(CC3)CC2)CC1)

`REAL300025051512.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051512.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051512/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051512 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3(CC3)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 19, 58, 69, 137, 137, 137, 137, 137, 5, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 1, 1, 58, 58, 137, 19, 5, 5, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 46, 47, 48, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 364
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051512 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3(CC3)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 31, 13, 1, 1, 1, 1, 1, 1, 1, 68, 68, 122, 137, 137, 137, 137, 201, 201, 201, 201, 201, 201, 201, 137, 137, 31, 31, 1, 68, 122, 122, 137, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 137, 137, 137, 137] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 741
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051512 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3(CC3)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 148, 159, 201, 201, 201, 201, 201, 18, 14, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 148, 148, 201, 63, 18, 18, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14] 201
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 46, 47, 48, 49])
total number of confs: 682
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051512 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051512
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051512/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051512
Building REAL300025051513
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051513'
/scratch/stefan/7786831/working/building/REAL300025051513 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051513

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051513/0 /scratch/stefan/7786831/working/building/REAL300025051513 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 385)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/385
`/scratch/stefan/7786831/working/3D/385' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC3=CN=CC=C3C=C2)CC1)

`REAL300025051513.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051513.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051513/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051513 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC3=CN=CC=C3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 29, 96, 107, 197, 197, 197, 197, 197, 7, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 96, 96, 197, 29, 7, 7, 3, 7, 7, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 529
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051513 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC3=CN=CC=C3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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, 7]
0  hydrogens 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, 31, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 141, 197, 197, 197, 197, 201, 201, 201, 201, 201, 201, 201, 201, 201, 197, 197, 31, 31, 1, 65, 141, 141, 197, 201, 201, 201, 201, 201, 197, 197, 197, 197] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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])
total number of confs: 748
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051513 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC3=CN=CC=C3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [49, 49, 49, 128, 136, 201, 201, 201, 201, 201, 13, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 128, 128, 201, 49, 13, 13, 4, 1, 1, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43])
total number of confs: 619
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051513 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051513
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051513/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051513
Building REAL300025051514
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051514'
/scratch/stefan/7786831/working/building/REAL300025051514 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051514

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051514/0 /scratch/stefan/7786831/working/building/REAL300025051514 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 386)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/386
`/scratch/stefan/7786831/working/3D/386' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1CCCCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051514.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051514.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051514/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051514 none O=C(CCC1CCCCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 10, 13, 27, 27, 27, 27, 27, 27, 1, 1, 1, 4, 6, 6, 6, 17, 25, 74, 74, 74, 74, 74, 1, 1, 10, 10, 15, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 4, 4, 6, 17, 17, 74, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 51, 52, 53, 54, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 259
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051514 none O=C(CCC1CCCCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 6, 4, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 52, 66, 66, 66, 104, 135, 201, 201, 201, 201, 201, 27, 27, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 52, 52, 66, 104, 104, 201, 27, 27, 27, 27] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 39, 40, 35, 43, 41, 36, 38, 42, 37, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 668
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051514 none O=C(CCC1CCCCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [74, 74, 74, 157, 150, 201, 201, 201, 201, 201, 201, 74, 67, 40, 40, 21, 40, 12, 1, 1, 1, 1, 1, 1, 1, 74, 74, 157, 157, 158, 158, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 74, 67, 67, 40, 21, 21, 1, 74, 74, 74, 74] 201
rigid atoms, others: [50, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54])
total number of confs: 862
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051514 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051514
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051514/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051514
Building REAL300025051515
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051515'
/scratch/stefan/7786831/working/building/REAL300025051515 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051515

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051515/0 /scratch/stefan/7786831/working/building/REAL300025051515 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 387)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/387
`/scratch/stefan/7786831/working/3D/387' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=NC=CC=C3O2)CC1)

`REAL300025051515.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051515.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051515/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051515 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=NC=CC=C3O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 30, 117, 131, 201, 201, 201, 201, 201, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 117, 117, 201, 30, 6, 6, 3, 7, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 579
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051515 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=NC=CC=C3O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 143, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 32, 32, 1, 74, 143, 143, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 747
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051515 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=NC=CC=C3O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [35, 35, 35, 122, 135, 201, 201, 201, 201, 201, 10, 7, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 122, 122, 201, 35, 10, 10, 5, 1, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 580
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051515 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051515
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051515/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051515
Building REAL300025051516
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051516'
/scratch/stefan/7786831/working/building/REAL300025051516 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051516

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051516/0 /scratch/stefan/7786831/working/building/REAL300025051516 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 388)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/388
`/scratch/stefan/7786831/working/3D/388' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CNC(=O)C=C2)CC1)

`REAL300025051516.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051516.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051516/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051516 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CNC(=O)C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 11, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 17, 48, 57, 98, 98, 98, 98, 98, 5, 1, 1, 1, 3, 3, 3, 8, 16, 16, 16, 16, 16, 16, 1, 1, 48, 48, 98, 17, 5, 5, 3, 8, 8, 16, 16, 16, 16, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 299
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051516 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CNC(=O)C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 11, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 27, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 85, 98, 98, 98, 98, 131, 201, 201, 201, 201, 201, 201, 98, 98, 27, 27, 1, 61, 85, 85, 98, 131, 131, 201, 201, 201, 201, 98, 98, 98, 98] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 686
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051516 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CNC(=O)C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 11, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 145, 163, 201, 201, 201, 201, 201, 24, 16, 11, 11, 5, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 145, 145, 201, 67, 24, 24, 11, 5, 5, 1, 1, 1, 1, 16, 16, 16, 16] 201
rigid atoms, others: [35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42])
total number of confs: 684
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051516 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051516
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051516/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051516
Building REAL300025051517
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051517'
/scratch/stefan/7786831/working/building/REAL300025051517 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051517

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051517/0 /scratch/stefan/7786831/working/building/REAL300025051517 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 389)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/389
`/scratch/stefan/7786831/working/3D/389' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC(F)F)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051517.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051517.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051517/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051517 none CC(CC(F)F)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 15, 15, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [178, 90, 178, 198, 201, 201, 90, 90, 90, 73, 45, 45, 26, 45, 13, 1, 1, 1, 1, 1, 1, 1, 90, 90, 178, 178, 178, 178, 201, 201, 201, 90, 73, 73, 45, 26, 26, 1, 90, 90, 90, 90] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41])
total number of confs: 887
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051517 none CC(CC(F)F)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 15, 15, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 2, 11, 27, 52, 52, 2, 2, 1, 1, 1, 4, 12, 12, 12, 31, 36, 90, 90, 90, 90, 90, 1, 1, 11, 11, 11, 11, 29, 29, 52, 2, 4, 4, 12, 31, 31, 90, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 8, 9, 10, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
total number of confs: 440
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051517 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051517
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051517/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051517
Building REAL300025051518
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051518'
/scratch/stefan/7786831/working/building/REAL300025051518 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051518

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051518/0 /scratch/stefan/7786831/working/building/REAL300025051518 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 390)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/390
`/scratch/stefan/7786831/working/3D/390' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(F)=CN2)CC1)

`REAL300025051518.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051518.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051518/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051518 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(F)=CN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 15, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 19, 45, 49, 70, 70, 70, 70, 70, 5, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 1, 1, 45, 45, 70, 19, 5, 5, 3, 10, 10, 10, 1, 1, 1, 1] 70
rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 232
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051518 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(F)=CN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 15, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [34, 25, 12, 1, 1, 1, 1, 1, 1, 1, 34, 34, 58, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 25, 25, 1, 34, 58, 58, 70, 70, 70, 70, 70, 70, 70, 70] 70
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 263
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051518 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(F)=CN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 15, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 57, 59, 70, 70, 70, 70, 70, 17, 10, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 10, 57, 57, 70, 35, 17, 17, 6, 1, 1, 1, 10, 10, 10, 10] 70
rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37])
total number of confs: 257
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051518 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051518
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051518/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051518
Building REAL300025051519
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051519'
/scratch/stefan/7786831/working/building/REAL300025051519 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051519

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051519/0 /scratch/stefan/7786831/working/building/REAL300025051519 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 391)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/391
`/scratch/stefan/7786831/working/3D/391' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1)

`REAL300025051519.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051519.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051519/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051519 none CC1(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 12, 2, 2, 2, 1, 1, 1, 4, 11, 11, 11, 28, 32, 89, 89, 89, 89, 89, 1, 1, 30, 30, 30, 30, 30, 12, 12, 2, 4, 4, 11, 28, 28, 89, 1, 1, 1, 1, 30, 30, 30, 30] 201
rigid atoms, others: [35, 36, 5, 6, 7, 19, 20, 38, 37] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42])
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: REAL300025051519 none CC1(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 7, 30, 30, 30, 30, 55, 115, 115, 115, 163, 172, 201, 201, 201, 201, 201, 30, 30, 1, 1, 2, 2, 2, 7, 7, 30, 55, 55, 115, 163, 163, 201, 30, 30, 30, 30, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 39, 40, 41, 42, 21, 22] set([3, 4, 5, 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])
total number of confs: 734
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051519 none CC1(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 157, 89, 89, 89, 89, 76, 46, 46, 24, 46, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 201, 201, 201, 201, 201, 157, 157, 89, 76, 76, 46, 24, 24, 1, 89, 89, 89, 89, 201, 201, 201, 201] 201
rigid atoms, others: [34, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 845
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051519 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051519
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051519/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051519
Building REAL300025051520
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051520'
/scratch/stefan/7786831/working/building/REAL300025051520 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051520

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051520/0 /scratch/stefan/7786831/working/building/REAL300025051520 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 392)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/392
`/scratch/stefan/7786831/working/3D/392' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCC(CC)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051520.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051520.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051520/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051520 none CCCCC(CC)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 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.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 180, 156, 177, 197, 85, 85, 85, 85, 79, 57, 57, 38, 57, 13, 1, 1, 1, 1, 1, 1, 1, 85, 85, 201, 201, 201, 201, 201, 201, 201, 201, 201, 180, 197, 194, 197, 197, 197, 156, 156, 85, 79, 79, 57, 38, 38, 1, 85, 85, 85, 85] 201
rigid atoms, others: [49, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53])
total number of confs: 1034
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: REAL300025051520 none CCCCC(CC)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 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.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 27, 27, 17, 11, 17, 22, 2, 2, 2, 1, 1, 1, 4, 11, 11, 11, 26, 38, 85, 85, 85, 85, 85, 1, 1, 28, 28, 28, 28, 28, 27, 27, 27, 27, 18, 22, 21, 22, 22, 22, 11, 11, 2, 4, 4, 11, 26, 26, 85, 1, 1, 1, 1] 201
rigid atoms, others: [10, 11, 12, 50, 51, 52, 53, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 355
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051520 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051520
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051520/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051520
Building REAL300025051521
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051521'
/scratch/stefan/7786831/working/building/REAL300025051521 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051521

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051521/0 /scratch/stefan/7786831/working/building/REAL300025051521 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 393)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/393
`/scratch/stefan/7786831/working/3D/393' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC(=O)N1)

`REAL300025051521.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051521.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051521/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051521 none CCC1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 8, 8, 8, 2, 2, 2, 1, 1, 1, 7, 14, 14, 14, 38, 52, 148, 148, 148, 148, 148, 1, 1, 8, 8, 8, 8, 13, 13, 13, 13, 13, 8, 8, 8, 8, 2, 7, 7, 14, 38, 38, 148, 1, 1, 1, 1, 8, 8, 8] 201
rigid atoms, others: [7, 8, 9, 43, 44, 45, 46, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 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, 41, 42, 47, 48, 49])
total number of confs: 355
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: REAL300025051521 none CCC1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 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: [4, 1, 1, 1, 1, 1, 8, 8, 8, 8, 19, 30, 30, 30, 73, 90, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 19, 19, 30, 73, 73, 201, 8, 8, 8, 8, 1, 1, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 33, 34, 47, 48, 49, 35, 23, 24, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 516
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051521 none CCC1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 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, 148, 148, 148, 148, 110, 65, 65, 29, 65, 13, 1, 1, 1, 1, 1, 1, 1, 148, 148, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 148, 110, 110, 65, 29, 29, 1, 148, 148, 148, 148, 201, 201, 201] 201
rigid atoms, others: [42, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 727
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051521 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051521
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051521/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051521
Building REAL300025051522
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051522'
/scratch/stefan/7786831/working/building/REAL300025051522 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051522

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051522/0 /scratch/stefan/7786831/working/building/REAL300025051522 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 394)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/394
`/scratch/stefan/7786831/working/3D/394' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2(CCF)CC2)CC1)

`REAL300025051522.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051522.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051522/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051522 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2(CCF)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 14, 16, 31, 31, 31, 31, 31, 5, 1, 1, 1, 3, 3, 3, 11, 27, 37, 11, 11, 1, 1, 14, 14, 31, 9, 5, 5, 3, 27, 27, 37, 37, 11, 11, 11, 11, 1, 1, 1, 1] 71
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 242
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: REAL300025051522 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2(CCF)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [25, 15, 11, 1, 1, 1, 1, 1, 1, 1, 25, 25, 30, 31, 31, 31, 31, 54, 71, 71, 54, 54, 31, 31, 15, 15, 1, 25, 30, 30, 31, 71, 71, 71, 71, 54, 54, 54, 54, 31, 31, 31, 31] 71
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 277
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051522 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2(CCF)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 32, 34, 54, 54, 54, 54, 54, 14, 11, 7, 7, 1, 7, 1, 1, 7, 13, 1, 1, 11, 11, 32, 32, 54, 24, 14, 14, 7, 7, 7, 13, 13, 1, 1, 1, 1, 11, 11, 11, 11] 71
rigid atoms, others: [35, 36, 37, 38, 14, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42])
total number of confs: 217
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051522 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051522
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051522/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051522
Building REAL300025051523
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051523'
/scratch/stefan/7786831/working/building/REAL300025051523 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051523

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051523/0 /scratch/stefan/7786831/working/building/REAL300025051523 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 395)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/395
`/scratch/stefan/7786831/working/3D/395' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(C)(C)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051523.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051523.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051523/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051523 none COCC(C)(C)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 200, 180, 200, 200, 132, 132, 132, 132, 115, 85, 85, 31, 85, 13, 1, 1, 1, 1, 1, 1, 1, 132, 132, 201, 201, 201, 201, 201, 200, 200, 200, 200, 200, 200, 180, 180, 132, 115, 115, 85, 31, 31, 1, 132, 132, 132, 132] 201
rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48])
total number of confs: 875
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051523 none COCC(C)(C)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 12, 9, 5, 9, 9, 2, 2, 2, 1, 1, 1, 4, 8, 8, 8, 27, 50, 132, 132, 132, 132, 132, 1, 1, 18, 18, 18, 12, 12, 9, 9, 9, 9, 9, 9, 5, 5, 2, 4, 4, 8, 27, 27, 132, 1, 1, 1, 1] 201
rigid atoms, others: [9, 10, 11, 45, 46, 47, 48, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 318
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051523 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051523
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051523/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051523
Building REAL300025051524
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051524'
/scratch/stefan/7786831/working/building/REAL300025051524 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051524

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051524/0 /scratch/stefan/7786831/working/building/REAL300025051524 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 396)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/396
`/scratch/stefan/7786831/working/3D/396' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CN(C)N=C1)

`REAL300025051524.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051524.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051524/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051524 none CC(CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CN(C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [165, 142, 83, 83, 83, 83, 69, 55, 55, 37, 55, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 165, 201, 201, 201, 201, 201, 165, 165, 165, 165, 142, 142, 83, 69, 69, 55, 37, 37, 1, 83, 83, 83, 83, 201, 201, 201, 201, 201] 201
rigid atoms, others: [39, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 817
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051524 none CC(CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CN(C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 5, 2, 2, 2, 1, 1, 1, 4, 11, 11, 11, 30, 39, 83, 83, 83, 83, 83, 1, 1, 9, 19, 19, 19, 19, 19, 9, 9, 9, 9, 5, 5, 2, 4, 4, 11, 30, 30, 83, 1, 1, 1, 1, 19, 19, 19, 19, 19] 201
rigid atoms, others: [5, 6, 7, 40, 41, 42, 43, 19, 20] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48])
total number of confs: 242
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051524 none CC(CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CN(C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 9, 19, 19, 19, 19, 34, 64, 64, 64, 114, 141, 201, 201, 201, 201, 201, 19, 19, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 9, 9, 19, 34, 34, 64, 114, 114, 201, 19, 19, 19, 19, 1, 2, 2, 2, 1] 201
rigid atoms, others: [1, 44, 48, 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, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47])
total number of confs: 654
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051524 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051524
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051524/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051524
Building REAL300025051525
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051525'
/scratch/stefan/7786831/working/building/REAL300025051525 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051525

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051525/0 /scratch/stefan/7786831/working/building/REAL300025051525 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 397)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/397
`/scratch/stefan/7786831/working/3D/397' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC=CC(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1)

`REAL300025051525.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051525.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051525/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051525 none CC1=NC=CC(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 1, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 27, 27, 27, 14, 9, 2, 2, 2, 1, 1, 1, 7, 18, 18, 18, 48, 67, 143, 143, 143, 143, 143, 1, 1, 27, 27, 27, 27, 27, 27, 14, 14, 9, 9, 2, 7, 7, 18, 48, 48, 143, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051525 none CC1=NC=CC(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 1, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 10, 27, 27, 27, 27, 37, 60, 60, 60, 112, 134, 201, 201, 201, 201, 201, 27, 27, 1, 2, 2, 2, 1, 1, 6, 6, 10, 10, 27, 37, 37, 60, 112, 112, 201, 27, 27, 27, 27] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 668
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051525 none CC1=NC=CC(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 1, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 184, 182, 143, 143, 143, 143, 110, 58, 58, 27, 58, 13, 1, 1, 1, 1, 1, 1, 1, 143, 143, 201, 201, 201, 201, 201, 201, 184, 184, 182, 182, 143, 110, 110, 58, 27, 27, 1, 143, 143, 143, 143] 201
rigid atoms, others: [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, 40, 41, 43, 44, 45, 46])
total number of confs: 765
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051525 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051525
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051525/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051525
Building REAL300025051526
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051526'
/scratch/stefan/7786831/working/building/REAL300025051526 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051526

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051526/0 /scratch/stefan/7786831/working/building/REAL300025051526 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 398)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/398
`/scratch/stefan/7786831/working/3D/398' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=NN(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1=O)

`REAL300025051526.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051526.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051526/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051526 none CN1C=NN(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 8, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 38, 38, 38, 17, 10, 2, 2, 2, 1, 1, 1, 4, 8, 8, 8, 27, 50, 101, 101, 101, 101, 101, 1, 1, 38, 38, 38, 38, 38, 38, 17, 17, 10, 10, 2, 4, 4, 8, 27, 27, 101, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
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: REAL300025051526 none CN1C=NN(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 8, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 12, 37, 38, 38, 38, 52, 71, 71, 71, 116, 142, 201, 201, 201, 201, 201, 38, 38, 1, 1, 2, 2, 2, 1, 6, 6, 12, 12, 38, 52, 52, 71, 116, 116, 201, 38, 38, 38, 38] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 26, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051526 none CN1C=NN(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 8, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 188, 179, 101, 101, 101, 101, 85, 60, 60, 24, 60, 12, 1, 1, 1, 1, 1, 1, 1, 101, 101, 201, 201, 201, 201, 201, 201, 188, 188, 179, 179, 101, 85, 85, 60, 24, 24, 1, 101, 101, 101, 101] 201
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 797
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051526 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051526
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051526/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051526
Building REAL300025051527
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051527'
/scratch/stefan/7786831/working/building/REAL300025051527 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051527

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051527/0 /scratch/stefan/7786831/working/building/REAL300025051527 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 399)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/399
`/scratch/stefan/7786831/working/3D/399' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(COCC(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051527.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051527.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051527/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051527 none O=C(COCC(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 5, 5, 15, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [94, 94, 94, 156, 178, 201, 201, 201, 94, 80, 52, 52, 25, 52, 13, 1, 1, 1, 1, 1, 1, 1, 94, 94, 156, 156, 201, 201, 201, 94, 80, 80, 52, 25, 25, 1, 94, 94, 94, 94] 201
rigid atoms, others: [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, 33, 34, 36, 37, 38, 39])
total number of confs: 878
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051527 none O=C(COCC(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 5, 5, 15, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 5, 10, 27, 42, 42, 1, 1, 1, 3, 5, 5, 5, 16, 27, 94, 94, 94, 94, 94, 1, 1, 5, 5, 27, 27, 42, 2, 3, 3, 5, 16, 16, 94, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 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/7786831/working/building/REAL300025051527 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051527
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051527/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051527
Building REAL300025051528
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051528'
/scratch/stefan/7786831/working/building/REAL300025051528 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051528

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051528/0 /scratch/stefan/7786831/working/building/REAL300025051528 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 400)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/400
`/scratch/stefan/7786831/working/3D/400' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCCC1=NNN=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051528.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051528.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051528/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051528 none O=C(CCCCC1=NNN=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 1, 8, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 10, 15, 18, 20, 48, 48, 48, 48, 1, 1, 1, 3, 5, 5, 5, 22, 35, 98, 98, 98, 98, 98, 1, 1, 10, 10, 18, 18, 18, 18, 20, 20, 48, 48, 2, 3, 3, 5, 22, 22, 98, 1, 1, 1, 1] 201
rigid atoms, others: [44, 11, 12, 13, 46, 45, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
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: REAL300025051528 none O=C(CCCCC1=NNN=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 1, 8, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [48, 16, 8, 8, 6, 1, 1, 1, 1, 1, 1, 48, 48, 48, 61, 70, 70, 70, 111, 139, 201, 201, 201, 201, 201, 48, 48, 16, 16, 8, 8, 8, 8, 6, 6, 1, 1, 48, 61, 61, 70, 111, 111, 201, 48, 48, 48, 48] 201
rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 660
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051528 none O=C(CCCCC1=NNN=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 1, 8, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [98, 98, 98, 176, 184, 189, 190, 201, 201, 201, 201, 98, 88, 65, 65, 30, 65, 13, 1, 1, 1, 1, 1, 1, 1, 98, 98, 176, 176, 189, 189, 189, 189, 190, 190, 201, 201, 98, 88, 88, 65, 30, 30, 1, 98, 98, 98, 98] 201
rigid atoms, others: [43, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47])
total number of confs: 849
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051528 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051528/1 /scratch/stefan/7786831/working/building/REAL300025051528 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 401)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/401
`/scratch/stefan/7786831/working/3D/401' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCCC1=CNN=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051528.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051528.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051528/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051528 none O=C(CCCCC1=CNN=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 1, 1, 8, 8, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 9, 13, 15, 19, 31, 31, 31, 31, 1, 1, 1, 4, 5, 5, 5, 23, 48, 131, 131, 131, 131, 131, 1, 1, 9, 9, 15, 15, 15, 15, 19, 19, 31, 31, 2, 4, 4, 5, 23, 23, 131, 1, 1, 1, 1] 201
rigid atoms, others: [44, 11, 12, 13, 46, 45, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 352
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051528 none O=C(CCCCC1=CNN=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 1, 1, 8, 8, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 13, 8, 7, 6, 1, 1, 1, 1, 1, 1, 31, 31, 31, 35, 39, 39, 39, 86, 129, 201, 201, 201, 201, 201, 31, 31, 13, 13, 8, 8, 8, 8, 6, 6, 1, 1, 31, 35, 35, 39, 86, 86, 201, 31, 31, 31, 31] 201
rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 590
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051528 none O=C(CCCCC1=CNN=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 1, 1, 8, 8, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [131, 131, 131, 190, 189, 194, 199, 201, 201, 201, 201, 131, 108, 93, 93, 33, 93, 13, 1, 1, 1, 1, 1, 1, 1, 131, 131, 190, 190, 194, 194, 194, 194, 199, 199, 201, 201, 131, 108, 108, 93, 33, 33, 1, 131, 131, 131, 131] 201
rigid atoms, others: [43, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47])
total number of confs: 835
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051528 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051528
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051528/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051528/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051528
Building REAL300025051529
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051529'
/scratch/stefan/7786831/working/building/REAL300025051529 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051529

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051529/0 /scratch/stefan/7786831/working/building/REAL300025051529 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 402)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/402
`/scratch/stefan/7786831/working/3D/402' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CO1)

`REAL300025051529.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051529.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051529/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051529 none NC(=O)C1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CO1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 12, 6, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 20, 20, 20, 68, 77, 124, 124, 124, 124, 124, 1, 1, 5, 5, 5, 5, 5, 2, 4, 4, 20, 68, 68, 124, 1, 1, 1, 1, 5] 201
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40])
total number of confs: 353
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051529 none NC(=O)C1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CO1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 12, 6, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 56, 56, 56, 142, 154, 201, 201, 201, 201, 201, 5, 5, 1, 1, 2, 2, 1, 5, 13, 13, 56, 142, 142, 201, 5, 5, 5, 5, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 40, 24, 25, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 653
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051529 none NC(=O)C1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CO1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 12, 6, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 124, 124, 124, 101, 52, 52, 23, 52, 11, 1, 1, 1, 1, 1, 1, 1, 124, 124, 201, 201, 201, 201, 201, 124, 101, 101, 52, 23, 23, 1, 124, 124, 124, 124, 201] 201
rigid atoms, others: [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, 33, 34, 36, 37, 38, 39, 40])
total number of confs: 597
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051529 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051529
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051529/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051529
Building REAL300025051530
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051530'
/scratch/stefan/7786831/working/building/REAL300025051530 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051530

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051530/0 /scratch/stefan/7786831/working/building/REAL300025051530 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 403)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/403
`/scratch/stefan/7786831/working/3D/403' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)N=N1)

`REAL300025051530.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051530.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051530/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051530 none CCC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 9, 9, 9, 2, 2, 2, 1, 1, 1, 4, 6, 6, 6, 17, 28, 93, 93, 93, 93, 93, 1, 1, 9, 9, 9, 9, 24, 24, 24, 24, 24, 9, 2, 4, 4, 6, 17, 17, 93, 1, 1, 1, 1, 9, 9, 9] 201
rigid atoms, others: [7, 8, 9, 42, 43, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 44, 45, 46])
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: REAL300025051530 none CCC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 1, 1, 1, 1, 9, 9, 9, 9, 15, 23, 23, 23, 46, 71, 134, 134, 134, 134, 134, 9, 9, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 9, 15, 15, 23, 46, 46, 134, 9, 9, 9, 9, 2, 2, 2] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 23, 24, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 365
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051530 none CCC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 134, 134, 134, 93, 93, 93, 93, 78, 50, 50, 30, 50, 13, 1, 1, 1, 1, 1, 1, 1, 93, 93, 134, 134, 134, 134, 201, 201, 201, 201, 201, 134, 93, 78, 78, 50, 30, 30, 1, 93, 93, 93, 93, 134, 134, 134] 201
rigid atoms, others: [39, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 860
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051530 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051530
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051530/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051530
Building REAL300025051531
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051531'
/scratch/stefan/7786831/working/building/REAL300025051531 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051531

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051531/0 /scratch/stefan/7786831/working/building/REAL300025051531 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 404)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/404
`/scratch/stefan/7786831/working/3D/404' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCCC2(F)F)CC1)

`REAL300025051531.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051531.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051531/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051531 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCCC2(F)F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 87, 102, 188, 188, 188, 188, 188, 6, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 1, 1, 87, 87, 188, 24, 6, 6, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 501
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051531 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCCC2(F)F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [79, 33, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 153, 188, 188, 188, 188, 201, 201, 201, 201, 201, 201, 201, 188, 188, 33, 33, 1, 79, 153, 153, 188, 201, 201, 201, 201, 201, 201, 201, 201, 201, 188, 188, 188, 188] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 763
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051531 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCCC2(F)F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 133, 144, 201, 201, 201, 201, 201, 19, 11, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 133, 133, 201, 57, 19, 19, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45])
total number of confs: 634
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051531 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051531
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051531/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051531
Building REAL300025051532
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051532'
/scratch/stefan/7786831/working/building/REAL300025051532 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051532

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051532/0 /scratch/stefan/7786831/working/building/REAL300025051532 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 405)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/405
`/scratch/stefan/7786831/working/3D/405' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)N1C=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051532.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051532.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051532/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051532 none CC(C)N1C=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 3, 7, 3, 3, 3, 2, 2, 2, 1, 1, 1, 7, 20, 20, 20, 67, 83, 192, 192, 192, 192, 192, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 3, 2, 7, 7, 20, 67, 67, 192, 1, 1, 1, 1, 3] 201
rigid atoms, others: [43, 9, 10, 11, 44, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45])
total number of confs: 474
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051532 none CC(C)N1C=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 2, 2, 3, 3, 9, 23, 23, 23, 74, 93, 201, 201, 201, 201, 201, 3, 3, 1, 4, 4, 4, 4, 4, 4, 4, 1, 3, 9, 9, 23, 74, 74, 201, 3, 3, 3, 3, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 33, 7, 45, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 509
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051532 none CC(C)N1C=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 192, 192, 192, 192, 121, 53, 53, 26, 53, 12, 1, 1, 1, 1, 1, 1, 1, 192, 192, 201, 201, 201, 201, 201, 201, 201, 201, 201, 192, 121, 121, 53, 26, 26, 1, 192, 192, 192, 192, 201] 201
rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45])
total number of confs: 726
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051532 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051532
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051532/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051532
Building REAL300025051533
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051533'
/scratch/stefan/7786831/working/building/REAL300025051533 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051533

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051533/0 /scratch/stefan/7786831/working/building/REAL300025051533 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 406)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/406
`/scratch/stefan/7786831/working/3D/406' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+](C)C1(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCCC1)

`REAL300025051533.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051533.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051533/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051533 none C[NH+](C)C1(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 4, 6, 6, 6, 9, 11, 17, 17, 17, 17, 17, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 6, 9, 9, 17, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4] 17
rigid atoms, others: [8, 9, 10, 43, 44, 45, 46, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 62
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: REAL300025051533 none C[NH+](C)C1(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 2, 1, 1, 3, 4, 4, 4, 4, 5, 8, 8, 8, 12, 13, 17, 17, 17, 17, 17, 4, 4, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 4, 5, 5, 8, 12, 12, 17, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1] 17
rigid atoms, others: [1, 4, 5, 47, 48, 49, 50, 51, 52, 53, 54, 24, 25, 26, 27] set([0, 2, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 72
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051533 none C[NH+](C)C1(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 16, 16, 13, 16, 8, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 16, 13, 13, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17
rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 54
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051533 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051533
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051533/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051533
Building REAL300025051534
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051534'
/scratch/stefan/7786831/working/building/REAL300025051534 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051534

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051534/0 /scratch/stefan/7786831/working/building/REAL300025051534 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 407)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/407
`/scratch/stefan/7786831/working/3D/407' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNS(=O)(=O)NCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051534.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051534.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051534/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051534 none CNS(=O)(=O)NCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 14, 11, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 6, 6, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 194, 130, 130, 130, 130, 92, 58, 58, 26, 58, 12, 1, 1, 1, 1, 1, 1, 1, 130, 130, 201, 201, 201, 201, 201, 194, 194, 130, 92, 92, 58, 26, 26, 1, 130, 130, 130, 130] 201
rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 847
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051534 none CNS(=O)(=O)NCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 14, 11, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 6, 6, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 15, 12, 15, 15, 7, 2, 2, 2, 1, 1, 1, 6, 9, 9, 9, 27, 40, 130, 130, 130, 130, 130, 1, 1, 22, 22, 22, 22, 12, 7, 7, 2, 6, 6, 9, 27, 27, 130, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 330
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051534 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051534
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051534/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051534
Building REAL300025051535
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051535'
/scratch/stefan/7786831/working/building/REAL300025051535 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051535

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051535/0 /scratch/stefan/7786831/working/building/REAL300025051535 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 408)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/408
`/scratch/stefan/7786831/working/3D/408' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCNC(=O)CC2)CC1)

`REAL300025051535.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051535.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051535/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051535 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCNC(=O)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 73, 89, 173, 173, 173, 173, 173, 5, 1, 1, 1, 3, 3, 3, 16, 16, 16, 16, 16, 16, 16, 1, 1, 73, 73, 173, 22, 5, 5, 3, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 464
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051535 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCNC(=O)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [83, 35, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 140, 173, 173, 173, 173, 201, 201, 201, 201, 201, 201, 201, 173, 173, 35, 35, 1, 83, 140, 140, 173, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 173, 173, 173, 173] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 740
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051535 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCNC(=O)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [62, 62, 62, 140, 150, 201, 201, 201, 201, 201, 22, 16, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 140, 140, 201, 62, 22, 22, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44, 45, 46])
total number of confs: 655
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051535 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051535
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051535/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051535
Building REAL300025051536
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051536'
/scratch/stefan/7786831/working/building/REAL300025051536 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051536

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051536/0 /scratch/stefan/7786831/working/building/REAL300025051536 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 409)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/409
`/scratch/stefan/7786831/working/3D/409' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=NC3=CC=NC=C32)CC1)

`REAL300025051536.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051536.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051536/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051536 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=NC3=CC=NC=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 21, 21, 60, 72, 153, 153, 153, 153, 153, 5, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 60, 60, 153, 21, 5, 5, 3, 15, 15, 15, 15, 15, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 381
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051536 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=NC3=CC=NC=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 35, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 128, 153, 153, 153, 153, 201, 201, 201, 201, 201, 201, 201, 201, 201, 153, 153, 35, 35, 1, 72, 128, 128, 153, 201, 201, 201, 201, 201, 153, 153, 153, 153] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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])
total number of confs: 642
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051536 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=NC3=CC=NC=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 142, 157, 201, 201, 201, 201, 201, 23, 15, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 142, 142, 201, 71, 23, 23, 9, 1, 1, 1, 1, 1, 15, 15, 15, 15] 201
rigid atoms, others: [35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43])
total number of confs: 667
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051536 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051536
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051536/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051536
Building REAL300025051537
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051537'
/scratch/stefan/7786831/working/building/REAL300025051537 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051537

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051537/0 /scratch/stefan/7786831/working/building/REAL300025051537 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 410)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/410
`/scratch/stefan/7786831/working/3D/410' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCCC3=CO2)CC1)

`REAL300025051537.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051537.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051537/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051537 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCCC3=CO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 29, 97, 114, 199, 199, 199, 199, 199, 6, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 1, 1, 97, 97, 199, 29, 6, 6, 3, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 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: REAL300025051537 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCCC3=CO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 30, 13, 1, 1, 1, 1, 1, 1, 1, 58, 58, 140, 199, 199, 199, 199, 201, 201, 201, 201, 201, 201, 201, 199, 199, 30, 30, 1, 58, 140, 140, 199, 201, 201, 201, 201, 201, 201, 201, 199, 199, 199, 199] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 744
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051537 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCCC3=CO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [51, 51, 51, 126, 140, 201, 201, 201, 201, 201, 16, 10, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 126, 126, 201, 51, 16, 16, 7, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43])
total number of confs: 613
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051537 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051537
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051537/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051537
Building REAL300025051538
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051538'
/scratch/stefan/7786831/working/building/REAL300025051538 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051538

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051538/0 /scratch/stefan/7786831/working/building/REAL300025051538 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 411)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/411
`/scratch/stefan/7786831/working/3D/411' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCOCC3=CO2)CC1)

`REAL300025051538.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051538.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051538/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051538 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCOCC3=CO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 5, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 29, 100, 114, 201, 201, 201, 201, 201, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 100, 100, 201, 29, 6, 6, 3, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 42, 11, 12, 13, 44, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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])
total number of confs: 540
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051538 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCOCC3=CO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 5, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 31, 13, 1, 1, 1, 1, 1, 1, 1, 57, 57, 139, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 31, 31, 1, 57, 139, 139, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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: 731
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051538 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCOCC3=CO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 5, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [49, 49, 49, 132, 143, 201, 201, 201, 201, 201, 12, 7, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 132, 132, 201, 49, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44])
total number of confs: 627
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051538 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051538
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051538/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051538
Building REAL300025051539
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051539'
/scratch/stefan/7786831/working/building/REAL300025051539 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051539

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051539/0 /scratch/stefan/7786831/working/building/REAL300025051539 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 412)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/412
`/scratch/stefan/7786831/working/3D/412' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CN=CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051539.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051539.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051539/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051539 none CC1=CN=CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 5, 2, 2, 2, 1, 1, 1, 4, 14, 14, 14, 38, 54, 111, 111, 111, 111, 111, 1, 1, 12, 12, 12, 12, 12, 12, 5, 5, 2, 4, 4, 14, 38, 38, 111, 1, 1, 1, 1, 12] 201
rigid atoms, others: [43, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44])
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: REAL300025051539 none CC1=CN=CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 12, 12, 12, 12, 24, 58, 58, 58, 110, 132, 201, 201, 201, 201, 201, 12, 12, 1, 2, 2, 2, 1, 1, 5, 5, 12, 24, 24, 58, 110, 110, 201, 12, 12, 12, 12, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 44, 25, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 611
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051539 none CC1=CN=CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 156, 111, 111, 111, 111, 98, 75, 75, 33, 75, 13, 1, 1, 1, 1, 1, 1, 1, 111, 111, 201, 201, 201, 201, 201, 201, 156, 156, 111, 98, 98, 75, 33, 33, 1, 111, 111, 111, 111, 201] 201
rigid atoms, others: [39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44])
total number of confs: 754
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051539 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051539
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051539/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051539
Building REAL300025051540
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051540'
/scratch/stefan/7786831/working/building/REAL300025051540 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051540

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051540/0 /scratch/stefan/7786831/working/building/REAL300025051540 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 413)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/413
`/scratch/stefan/7786831/working/3D/413' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C=CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1)

`REAL300025051540.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051540.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051540/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051540 none CCN1C=CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 8, 8, 8, 8, 8, 2, 2, 2, 1, 1, 1, 4, 10, 10, 10, 27, 43, 92, 92, 92, 92, 92, 1, 1, 8, 18, 18, 18, 18, 18, 8, 8, 8, 8, 2, 4, 4, 10, 27, 27, 92, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
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: REAL300025051540 none CCN1C=CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 3, 8, 8, 8, 8, 13, 27, 27, 27, 56, 76, 122, 122, 122, 122, 122, 8, 8, 1, 5, 5, 5, 5, 5, 1, 1, 3, 3, 8, 13, 13, 27, 56, 56, 122, 8, 8, 8, 8] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 352
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051540 none CCN1C=CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 122, 122, 122, 122, 122, 92, 92, 92, 92, 84, 63, 63, 47, 63, 13, 1, 1, 1, 1, 1, 1, 1, 92, 92, 122, 201, 201, 201, 201, 201, 122, 122, 122, 122, 92, 84, 84, 63, 47, 47, 1, 92, 92, 92, 92] 201
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 978
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051540 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051540
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051540/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051540
Building REAL300025051541
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051541'
/scratch/stefan/7786831/working/building/REAL300025051541 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051541

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051541/0 /scratch/stefan/7786831/working/building/REAL300025051541 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 414)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/414
`/scratch/stefan/7786831/working/3D/414' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@]23C[C@H]2COC3)CC1)

`REAL300025051541.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051541.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051541/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051541 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@]23C[C@H]2COC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 12, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 25, 68, 80, 138, 138, 138, 138, 138, 5, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 1, 1, 68, 68, 138, 25, 5, 5, 3, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 377
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051541 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@]23C[C@H]2COC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 12, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 109, 138, 138, 138, 138, 201, 201, 201, 201, 201, 201, 138, 138, 32, 32, 1, 64, 109, 109, 138, 201, 201, 201, 201, 201, 201, 138, 138, 138, 138] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 607
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051541 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@]23C[C@H]2COC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 12, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 142, 158, 201, 201, 201, 201, 201, 17, 11, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 142, 142, 201, 65, 17, 17, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41])
total number of confs: 675
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051541 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051541
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051541/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051541
Building REAL300025051542
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051542'
/scratch/stefan/7786831/working/building/REAL300025051542 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051542

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051542/0 /scratch/stefan/7786831/working/building/REAL300025051542 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 415)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/415
`/scratch/stefan/7786831/working/3D/415' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3N=CNC3=CN=C2)CC1)

`REAL300025051542.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051542.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051542/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051542 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3N=CNC3=CN=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 29, 103, 115, 201, 201, 201, 201, 201, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 103, 103, 201, 29, 6, 6, 3, 7, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 542
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051542 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3N=CNC3=CN=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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, 31, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 149, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 31, 31, 1, 64, 149, 149, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 761
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051542 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3N=CNC3=CN=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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: [50, 50, 50, 138, 147, 201, 201, 201, 201, 201, 13, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 138, 138, 201, 50, 13, 13, 4, 1, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 636
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051542 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051542
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051542/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051542
Building REAL300025051543
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051543'
/scratch/stefan/7786831/working/building/REAL300025051543 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051543

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051543/0 /scratch/stefan/7786831/working/building/REAL300025051543 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 416)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/416
`/scratch/stefan/7786831/working/3D/416' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)N1N=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1)

`REAL300025051543.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051543.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051543/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051543 none CC(C)(C)N1N=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 3, 6, 6, 3, 3, 3, 2, 2, 2, 1, 1, 1, 7, 13, 13, 13, 46, 70, 198, 198, 198, 198, 198, 1, 1, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 7, 7, 13, 46, 46, 198, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 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: REAL300025051543 none CC(C)(C)N1N=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 3, 3, 3, 3, 9, 15, 15, 15, 50, 73, 201, 201, 201, 201, 201, 3, 3, 1, 4, 4, 4, 3, 3, 3, 4, 4, 4, 3, 9, 9, 15, 50, 50, 201, 3, 3, 3, 3] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 26] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 431
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051543 none CC(C)(C)N1N=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 198, 198, 198, 198, 155, 66, 66, 30, 66, 13, 1, 1, 1, 1, 1, 1, 1, 198, 198, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 198, 155, 155, 66, 30, 30, 1, 198, 198, 198, 198] 201
rigid atoms, others: [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, 40, 41, 43, 44, 45, 46])
total number of confs: 772
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051543 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051543
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051543/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051543
Building REAL300025051544
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051544'
/scratch/stefan/7786831/working/building/REAL300025051544 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300025051544 as failed and skipping
/scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `/scratch/stefan/7786831/failed'
`/scratch/stefan/7786831/working/building/REAL300025051544' -> `/scratch/stefan/7786831/failed/REAL300025051544'
Building REAL300025051545
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051545'
/scratch/stefan/7786831/working/building/REAL300025051545 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051545

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051545/0 /scratch/stefan/7786831/working/building/REAL300025051545 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 417)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/417
`/scratch/stefan/7786831/working/3D/417' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC3=NC=CC=C3C=C2)CC1)

`REAL300025051545.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051545.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051545/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051545 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC3=NC=CC=C3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 30, 93, 98, 201, 201, 201, 201, 201, 7, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 93, 93, 201, 30, 7, 7, 3, 5, 5, 5, 5, 5, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 527
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051545 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC3=NC=CC=C3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 31, 13, 1, 1, 1, 1, 1, 1, 1, 55, 55, 147, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 31, 31, 1, 55, 147, 147, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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])
total number of confs: 739
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051545 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC3=NC=CC=C3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [47, 47, 47, 131, 136, 201, 201, 201, 201, 201, 11, 5, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 131, 131, 201, 47, 11, 11, 4, 1, 1, 1, 1, 1, 5, 5, 5, 5] 201
rigid atoms, others: [35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43])
total number of confs: 630
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051545 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051545
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051545/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051545
Building REAL300025051546
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051546'
/scratch/stefan/7786831/working/building/REAL300025051546 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051546

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051546/0 /scratch/stefan/7786831/working/building/REAL300025051546 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 418)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/418
`/scratch/stefan/7786831/working/3D/418' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CC=C(F)C=C2F)CC1)

`REAL300025051546.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051546.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051546/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051546 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CC=C(F)C=C2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 17, 49, 57, 132, 132, 132, 132, 132, 5, 1, 1, 1, 3, 3, 3, 17, 26, 26, 18, 26, 26, 26, 26, 1, 1, 49, 49, 132, 17, 5, 5, 3, 17, 17, 26, 26, 26, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 400
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051546 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CC=C(F)C=C2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [65, 30, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 111, 132, 132, 132, 132, 194, 201, 201, 195, 201, 201, 201, 201, 132, 132, 30, 30, 1, 65, 111, 111, 132, 194, 194, 201, 201, 201, 132, 132, 132, 132] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 823
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051546 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CC=C(F)C=C2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [69, 69, 69, 132, 139, 201, 201, 201, 201, 201, 36, 26, 19, 19, 5, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 132, 132, 201, 69, 36, 36, 19, 5, 5, 1, 1, 1, 26, 26, 26, 26] 201
rigid atoms, others: [36, 37, 38, 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, 39, 40, 41, 42])
total number of confs: 660
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051546 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051546
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051546/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051546
Building REAL300025051547
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051547'
/scratch/stefan/7786831/working/building/REAL300025051547 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051547

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051547/0 /scratch/stefan/7786831/working/building/REAL300025051547 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 419)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/419
`/scratch/stefan/7786831/working/3D/419' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(F)C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051547.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051547.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051547/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051547 none CC1=C(F)C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 15, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 6, 19, 19, 19, 52, 66, 137, 137, 137, 137, 137, 1, 1, 9, 9, 9, 9, 9, 9, 2, 6, 6, 19, 52, 52, 137, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 10, 11, 12, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
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: REAL300025051547 none CC1=C(F)C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 15, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 29, 64, 64, 64, 114, 126, 201, 201, 201, 201, 201, 9, 9, 2, 2, 2, 1, 1, 1, 9, 29, 29, 64, 114, 114, 201, 9, 9, 9, 9] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([9, 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, 41, 42])
total number of confs: 611
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051547 none CC1=C(F)C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 15, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 137, 137, 137, 137, 99, 53, 53, 25, 53, 13, 1, 1, 1, 1, 1, 1, 1, 137, 137, 201, 201, 201, 201, 201, 201, 137, 99, 99, 53, 25, 25, 1, 137, 137, 137, 137] 201
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42])
total number of confs: 614
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051547 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051547
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051547/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051547
Building REAL300025051548
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051548'
/scratch/stefan/7786831/working/building/REAL300025051548 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051548

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051548/0 /scratch/stefan/7786831/working/building/REAL300025051548 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 420)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/420
`/scratch/stefan/7786831/working/3D/420' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1F)

`REAL300025051548.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051548.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051548/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051548 none CC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 2, 5, 5, 2, 2, 2, 1, 1, 1, 7, 27, 27, 27, 80, 94, 190, 191, 191, 191, 191, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 2, 7, 7, 27, 80, 80, 191, 1, 1, 1, 1] 201
rigid atoms, others: [39, 8, 9, 10, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 504
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051548 none CC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 19, 59, 59, 59, 137, 147, 200, 201, 201, 201, 201, 5, 5, 1, 1, 2, 2, 2, 1, 1, 1, 5, 19, 19, 59, 137, 137, 201, 5, 5, 5, 5] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 25, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 642
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051548 none CC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 191, 191, 191, 191, 121, 50, 50, 27, 50, 13, 1, 1, 1, 1, 1, 1, 1, 191, 191, 201, 201, 201, 201, 201, 201, 201, 201, 191, 121, 121, 50, 27, 27, 1, 191, 191, 191, 191] 201
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42])
total number of confs: 724
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051548 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051548
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051548/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051548
Building REAL300025051549
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051549'
/scratch/stefan/7786831/working/building/REAL300025051549 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051549

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051549/0 /scratch/stefan/7786831/working/building/REAL300025051549 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 421)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/421
`/scratch/stefan/7786831/working/3D/421' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(Cl)C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051549.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051549.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051549/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051549 none CC1=C(Cl)C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 16, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 9, 3, 9, 9, 2, 2, 2, 1, 1, 1, 6, 20, 20, 20, 53, 67, 139, 140, 140, 140, 140, 1, 1, 9, 9, 9, 9, 9, 9, 2, 6, 6, 20, 53, 53, 140, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 10, 11, 12, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
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: REAL300025051549 none CC1=C(Cl)C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 16, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 27, 62, 62, 62, 112, 125, 200, 201, 201, 201, 201, 9, 9, 2, 2, 2, 1, 1, 1, 9, 27, 27, 62, 112, 112, 201, 9, 9, 9, 9] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([9, 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, 41, 42])
total number of confs: 608
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051549 none CC1=C(Cl)C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 16, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 140, 140, 140, 140, 101, 54, 54, 26, 54, 13, 1, 1, 1, 1, 1, 1, 1, 140, 140, 201, 201, 201, 201, 201, 201, 140, 101, 101, 54, 26, 26, 1, 140, 140, 140, 140] 201
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42])
total number of confs: 622
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051549 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051549
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051549/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051549
Building REAL300025051550
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051550'
/scratch/stefan/7786831/working/building/REAL300025051550 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051550

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051550/0 /scratch/stefan/7786831/working/building/REAL300025051550 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 422)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/422
`/scratch/stefan/7786831/working/3D/422' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C(Cl)C=CS2)CC1)

`REAL300025051550.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051550.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051550/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051550 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C(Cl)C=CS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 16, 1, 1, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 19, 56, 66, 107, 107, 107, 107, 107, 5, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 56, 56, 107, 19, 5, 5, 3, 13, 13, 1, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 304
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051550 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C(Cl)C=CS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 16, 1, 1, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [56, 27, 13, 1, 1, 1, 1, 1, 1, 1, 56, 56, 96, 107, 107, 107, 107, 201, 201, 201, 201, 201, 107, 107, 27, 27, 1, 56, 96, 96, 107, 201, 201, 107, 107, 107, 107] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 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])
total number of confs: 562
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051550 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C(Cl)C=CS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 16, 1, 1, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [65, 65, 65, 142, 161, 201, 201, 201, 201, 201, 20, 13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 13, 142, 142, 201, 65, 20, 20, 7, 1, 1, 13, 13, 13, 13] 201
rigid atoms, others: [32, 14, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36])
total number of confs: 645
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051550 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051550
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051550/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051550
Building REAL300025051551
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051551'
/scratch/stefan/7786831/working/building/REAL300025051551 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051551

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051551/0 /scratch/stefan/7786831/working/building/REAL300025051551 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 423)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/423
`/scratch/stefan/7786831/working/3D/423' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CNC=C2)CC1)

`REAL300025051551.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051551.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051551/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051551 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CNC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [18, 18, 18, 62, 75, 134, 134, 134, 134, 134, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 1, 1, 62, 62, 134, 18, 5, 5, 3, 9, 9, 9, 9, 1, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
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: REAL300025051551 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CNC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [70, 32, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 115, 134, 134, 134, 134, 201, 201, 201, 201, 134, 134, 32, 32, 1, 70, 115, 115, 134, 201, 201, 201, 201, 134, 134, 134, 134] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 25] set([0, 1, 2, 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])
total number of confs: 645
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051551 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CNC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [63, 63, 63, 144, 155, 201, 201, 201, 201, 201, 16, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 9, 9, 144, 144, 201, 63, 16, 16, 5, 1, 1, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37])
total number of confs: 659
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051551 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051551
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051551/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051551
Building REAL300025051552
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051552'
/scratch/stefan/7786831/working/building/REAL300025051552 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051552

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051552/0 /scratch/stefan/7786831/working/building/REAL300025051552 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 424)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/424
`/scratch/stefan/7786831/working/3D/424' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCCC1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051552.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051552.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051552/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051552 none CC1CCCC1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 6, 6, 6, 2, 2, 2, 1, 1, 1, 6, 16, 16, 16, 48, 56, 148, 148, 148, 148, 148, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 6, 6, 16, 48, 48, 148, 1, 1, 1, 1] 201
rigid atoms, others: [9, 10, 11, 45, 46, 47, 48, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 350
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051552 none CC1CCCC1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 20, 46, 46, 46, 116, 129, 201, 201, 201, 201, 201, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 20, 20, 46, 116, 116, 201, 6, 6, 6, 6] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 35, 33, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 630
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051552 none CC1CCCC1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 148, 148, 148, 148, 105, 49, 49, 27, 49, 12, 1, 1, 1, 1, 1, 1, 1, 148, 148, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 148, 105, 105, 49, 27, 27, 1, 148, 148, 148, 148] 201
rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48])
total number of confs: 876
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051552 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051552
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051552/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051552
Building REAL300025051553
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051553'
/scratch/stefan/7786831/working/building/REAL300025051553 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051553

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051553/0 /scratch/stefan/7786831/working/building/REAL300025051553 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 425)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/425
`/scratch/stefan/7786831/working/3D/425' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CNC(=O)C1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051553.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051553.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051553/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051553 none O=C(CNC(=O)C1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [2, 2, 2, 4, 4, 4, 4, 12, 12, 12, 12, 1, 1, 1, 5, 6, 6, 6, 10, 12, 23, 23, 23, 23, 23, 1, 1, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 5, 5, 6, 10, 10, 23, 1, 1, 1, 1] 41
rigid atoms, others: [11, 12, 13, 46, 47, 48, 49, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051553 none O=C(CNC(=O)C1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [12, 11, 8, 8, 1, 8, 1, 1, 1, 1, 1, 12, 12, 12, 13, 14, 14, 14, 25, 29, 41, 41, 41, 41, 41, 12, 12, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 13, 13, 14, 25, 25, 41, 12, 12, 12, 12] 41
rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 36, 38, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 129
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051553 none O=C(CNC(=O)C1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [23, 23, 23, 24, 24, 24, 24, 41, 41, 41, 41, 23, 23, 23, 23, 22, 23, 12, 1, 1, 1, 1, 1, 1, 1, 23, 23, 24, 24, 24, 41, 41, 41, 41, 41, 41, 41, 41, 41, 23, 23, 23, 23, 22, 22, 1, 23, 23, 23, 23] 41
rigid atoms, others: [45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49])
total number of confs: 129
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051553 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051553
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051553/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051553
Building REAL300025051554
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051554'
/scratch/stefan/7786831/working/building/REAL300025051554 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051554

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051554/0 /scratch/stefan/7786831/working/building/REAL300025051554 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 426)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/426
`/scratch/stefan/7786831/working/3D/426' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CNC(=O)C1=COC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051554.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051554.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051554/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051554 none O=C(CNC(=O)C1=COC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 8, 1, 11, 1, 1, 12, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 5, 6, 6, 6, 14, 14, 14, 14, 1, 1, 1, 6, 11, 11, 11, 35, 47, 83, 83, 83, 83, 83, 1, 1, 5, 5, 6, 14, 14, 14, 2, 6, 6, 11, 35, 35, 83, 1, 1, 1, 1] 116
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
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: REAL300025051554 none O=C(CNC(=O)C1=COC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 8, 1, 11, 1, 1, 12, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [14, 7, 5, 5, 1, 5, 1, 1, 1, 1, 1, 14, 14, 14, 23, 37, 37, 37, 80, 92, 116, 116, 116, 116, 116, 14, 14, 7, 7, 5, 1, 1, 1, 14, 23, 23, 37, 80, 80, 116, 14, 14, 14, 14] 116
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 408
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051554 none O=C(CNC(=O)C1=COC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 8, 1, 11, 1, 1, 12, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [83, 83, 83, 95, 95, 95, 95, 116, 116, 116, 116, 83, 76, 68, 68, 47, 68, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 95, 95, 95, 116, 116, 116, 83, 76, 76, 68, 47, 47, 1, 83, 83, 83, 83] 116
rigid atoms, others: [39, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 415
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051554 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051554
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051554/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051554
Building REAL300025051555
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051555'
/scratch/stefan/7786831/working/building/REAL300025051555 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051555

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051555/0 /scratch/stefan/7786831/working/building/REAL300025051555 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 427)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/427
`/scratch/stefan/7786831/working/3D/427' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)NC(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051555.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051555.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051555/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051555 none CCC(=O)NC(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 169, 169, 169, 166, 101, 166, 101, 101, 101, 85, 59, 59, 32, 59, 13, 1, 1, 1, 1, 1, 1, 1, 101, 101, 201, 201, 201, 201, 201, 169, 166, 166, 166, 166, 101, 85, 85, 59, 32, 32, 1, 101, 101, 101, 101] 201
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 934
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051555 none CCC(=O)NC(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 8, 8, 8, 6, 2, 6, 2, 2, 1, 1, 1, 4, 7, 7, 7, 21, 34, 101, 101, 101, 101, 101, 1, 1, 38, 38, 38, 38, 38, 8, 6, 6, 6, 6, 2, 4, 4, 7, 21, 21, 101, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 329
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051555 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051555
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051555/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051555
Building REAL300025051556
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051556'
/scratch/stefan/7786831/working/building/REAL300025051556 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051556

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051556/0 /scratch/stefan/7786831/working/building/REAL300025051556 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 428)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/428
`/scratch/stefan/7786831/working/3D/428' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(=O)N(C)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051556.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051556.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051556/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051556 none CC(C)C(=O)N(C)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 198, 201, 190, 198, 142, 142, 142, 142, 127, 84, 84, 31, 84, 13, 1, 1, 1, 1, 1, 1, 1, 142, 142, 201, 201, 201, 201, 201, 201, 201, 198, 198, 198, 190, 190, 142, 127, 127, 84, 31, 31, 1, 142, 142, 142, 142] 201
rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48])
total number of confs: 836
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051556 none CC(C)C(=O)N(C)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 14, 23, 11, 14, 7, 11, 2, 2, 2, 1, 1, 1, 4, 7, 7, 7, 24, 46, 142, 142, 142, 142, 142, 1, 1, 23, 23, 23, 23, 23, 23, 23, 11, 11, 11, 7, 7, 2, 4, 4, 7, 24, 24, 142, 1, 1, 1, 1] 201
rigid atoms, others: [10, 11, 12, 45, 46, 47, 48, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 363
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051556 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051556
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051556/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051556
Building REAL300025051557
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051557'
/scratch/stefan/7786831/working/building/REAL300025051557 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051557

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051557/0 /scratch/stefan/7786831/working/building/REAL300025051557 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 429)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/429
`/scratch/stefan/7786831/working/3D/429' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCS(=O)(=O)NCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051557.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051557.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051557/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051557 none CCS(=O)(=O)NCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 14, 11, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 200, 201, 201, 186, 105, 105, 105, 105, 81, 49, 49, 25, 49, 13, 1, 1, 1, 1, 1, 1, 1, 105, 105, 201, 201, 201, 201, 201, 200, 186, 186, 105, 81, 81, 49, 25, 25, 1, 105, 105, 105, 105] 201
rigid atoms, others: [39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 854
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051557 none CCS(=O)(=O)NCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 14, 11, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 20, 14, 20, 20, 7, 2, 2, 2, 1, 1, 1, 6, 10, 10, 10, 26, 37, 105, 105, 105, 105, 105, 1, 1, 28, 28, 28, 28, 28, 14, 7, 7, 2, 6, 6, 10, 26, 26, 105, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 352
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051557 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051557
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051557/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051557
Building REAL300025051558
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051558'
/scratch/stefan/7786831/working/building/REAL300025051558 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051558

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051558/0 /scratch/stefan/7786831/working/building/REAL300025051558 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 430)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/430
`/scratch/stefan/7786831/working/3D/430' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)NCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051558.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051558.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051558/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051558 none CS(=O)(=O)NCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 14, 11, 11, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 191, 186, 119, 119, 119, 119, 101, 70, 70, 33, 70, 13, 1, 1, 1, 1, 1, 1, 1, 119, 119, 201, 201, 201, 201, 191, 191, 186, 186, 119, 101, 101, 70, 33, 33, 1, 119, 119, 119, 119] 201
rigid atoms, others: [39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 873
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051558 none CS(=O)(=O)NCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 14, 11, 11, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 22, 25, 25, 9, 7, 2, 2, 2, 1, 1, 1, 4, 6, 6, 6, 20, 31, 119, 119, 119, 119, 119, 1, 1, 25, 25, 25, 22, 9, 9, 7, 7, 2, 4, 4, 6, 20, 20, 119, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 301
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051558 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051558
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051558/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051558
Building REAL300025051559
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051559'
/scratch/stefan/7786831/working/building/REAL300025051559 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051559

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051559/0 /scratch/stefan/7786831/working/building/REAL300025051559 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 431)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/431
`/scratch/stefan/7786831/working/3D/431' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)S(C)(=O)=O)

`REAL300025051559.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051559.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051559/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051559 none CN(CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)S(C)(=O)=O NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 139, 139, 139, 139, 112, 78, 78, 30, 78, 13, 1, 1, 1, 1, 1, 1, 1, 139, 139, 201, 201, 201, 201, 201, 201, 201, 201, 201, 139, 112, 112, 78, 30, 30, 1, 139, 139, 139, 139, 201, 201, 201] 201
rigid atoms, others: [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, 34, 35, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 834
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051559 none CN(CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)S(C)(=O)=O NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 2, 2, 2, 1, 1, 1, 5, 11, 11, 11, 35, 61, 139, 139, 139, 139, 139, 1, 1, 10, 17, 17, 17, 10, 10, 10, 8, 8, 2, 5, 5, 11, 35, 35, 139, 1, 1, 1, 1, 17, 17, 17] 201
rigid atoms, others: [37, 6, 7, 40, 39, 19, 20, 38, 5] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43])
total number of confs: 353
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051559 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051559
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051559/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051559
Building REAL300025051560
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051560'
/scratch/stefan/7786831/working/building/REAL300025051560 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051560

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051560/0 /scratch/stefan/7786831/working/building/REAL300025051560 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 432)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/432
`/scratch/stefan/7786831/working/3D/432' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C(=O)C1CC1)

`REAL300025051560.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051560.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051560/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051560 none CN(CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C(=O)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 148, 103, 103, 103, 103, 93, 65, 65, 28, 65, 13, 1, 1, 1, 1, 1, 1, 1, 103, 103, 158, 161, 161, 201, 201, 158, 158, 158, 148, 148, 103, 93, 93, 65, 28, 28, 1, 103, 103, 103, 103, 201, 201, 201, 201, 201] 201
rigid atoms, others: [37, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 830
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051560 none CN(CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C(=O)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 2, 2, 2, 1, 1, 1, 5, 8, 8, 8, 24, 39, 103, 103, 103, 103, 103, 1, 1, 10, 15, 15, 23, 23, 10, 10, 10, 7, 7, 2, 5, 5, 8, 24, 24, 103, 1, 1, 1, 1, 23, 23, 23, 23, 23] 201
rigid atoms, others: [5, 38, 7, 40, 41, 39, 19, 20, 6] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46])
total number of confs: 296
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051560 none CN(CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C(=O)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 11, 23, 23, 23, 23, 33, 46, 46, 46, 97, 124, 201, 201, 201, 201, 201, 23, 23, 1, 5, 1, 1, 1, 7, 7, 7, 11, 11, 23, 33, 33, 46, 97, 97, 201, 23, 23, 23, 23, 1, 1, 1, 1, 1] 201
rigid atoms, others: [42, 43, 44, 45, 46, 21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 619
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051560 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051560
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051560/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051560
Building REAL300025051561
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051561'
/scratch/stefan/7786831/working/building/REAL300025051561 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051561

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051561/0 /scratch/stefan/7786831/working/building/REAL300025051561 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 433)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/433
`/scratch/stefan/7786831/working/3D/433' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)N(C)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051561.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051561.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051561/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051561 none COCC(=O)N(C)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 148, 147, 148, 143, 147, 98, 98, 98, 98, 74, 49, 49, 26, 49, 13, 1, 1, 1, 1, 1, 1, 1, 98, 98, 201, 201, 201, 201, 201, 147, 147, 147, 143, 143, 98, 74, 74, 49, 26, 26, 1, 98, 98, 98, 98] 201
rigid atoms, others: [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, 40, 41, 43, 44, 45, 46])
total number of confs: 931
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051561 none COCC(=O)N(C)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [37, 22, 9, 7, 9, 6, 7, 2, 2, 2, 1, 1, 1, 3, 5, 5, 5, 17, 29, 98, 98, 98, 98, 98, 1, 1, 37, 37, 37, 22, 22, 7, 7, 7, 6, 6, 2, 3, 3, 5, 17, 17, 98, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 288
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051561 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051561
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051561/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051561
Building REAL300025051562
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051562'
/scratch/stefan/7786831/working/building/REAL300025051562 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051562

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051562/0 /scratch/stefan/7786831/working/building/REAL300025051562 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 434)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/434
`/scratch/stefan/7786831/working/3D/434' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1=O)

`REAL300025051562.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051562.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051562/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051562 none CN1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 2, 2, 2, 1, 1, 1, 7, 19, 19, 19, 43, 58, 146, 146, 146, 146, 146, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 7, 7, 19, 43, 43, 146, 1, 1, 1, 1, 8, 8] 201
rigid atoms, others: [6, 38, 7, 8, 41, 39, 40, 20, 21] set([0, 1, 2, 3, 4, 5, 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, 36, 37, 42, 43])
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: REAL300025051562 none CN1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 8, 8, 27, 53, 53, 53, 105, 127, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 2, 2, 2, 1, 1, 1, 8, 27, 27, 53, 105, 105, 201, 8, 8, 8, 8, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 42, 43, 22, 23, 24, 28, 29, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 617
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051562 none CN1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 146, 146, 146, 146, 106, 58, 58, 27, 58, 13, 1, 1, 1, 1, 1, 1, 1, 146, 146, 201, 201, 201, 201, 201, 201, 201, 201, 201, 146, 106, 106, 58, 27, 27, 1, 146, 146, 146, 146, 201, 201] 201
rigid atoms, others: [37, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43])
total number of confs: 729
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051562 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051562
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051562/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051562
Building REAL300025051563
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051563'
/scratch/stefan/7786831/working/building/REAL300025051563 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051563

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051563/0 /scratch/stefan/7786831/working/building/REAL300025051563 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 435)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/435
`/scratch/stefan/7786831/working/3D/435' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1=O)

`REAL300025051563.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051563.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051563/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051563 none CCN1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 15, 15, 15, 34, 44, 107, 107, 107, 107, 107, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7, 4, 4, 4, 2, 7, 7, 15, 34, 34, 107, 1, 1, 1, 1, 4, 4] 201
rigid atoms, others: [7, 8, 9, 42, 43, 44, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 45, 46])
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: REAL300025051563 none CCN1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 4, 4, 4, 4, 14, 25, 25, 25, 50, 63, 127, 127, 127, 127, 127, 4, 4, 1, 1, 1, 3, 3, 3, 2, 2, 1, 1, 1, 4, 14, 14, 25, 50, 50, 127, 4, 4, 4, 4, 1, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 33, 45, 46, 23, 24, 25, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 353
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051563 none CCN1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 127, 127, 127, 107, 107, 107, 107, 81, 42, 42, 27, 42, 13, 1, 1, 1, 1, 1, 1, 1, 107, 107, 127, 127, 127, 201, 201, 201, 201, 201, 127, 127, 127, 107, 81, 81, 42, 27, 27, 1, 107, 107, 107, 107, 127, 127] 201
rigid atoms, others: [40, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46])
total number of confs: 914
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051563 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051563
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051563/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051563
Building REAL300025051564
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051564'
/scratch/stefan/7786831/working/building/REAL300025051564 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051564

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051564/0 /scratch/stefan/7786831/working/building/REAL300025051564 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 436)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/436
`/scratch/stefan/7786831/working/3D/436' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)NCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051564.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051564.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051564/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051564 none COCC(=O)NCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 175, 175, 175, 175, 158, 65, 65, 65, 65, 50, 46, 46, 26, 46, 12, 1, 1, 1, 1, 1, 1, 1, 65, 65, 201, 201, 201, 201, 201, 175, 175, 175, 158, 158, 65, 50, 50, 46, 26, 26, 1, 65, 65, 65, 65] 201
rigid atoms, others: [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, 40, 41, 43, 44, 45, 46])
total number of confs: 885
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051564 none COCC(=O)NCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [45, 32, 14, 14, 14, 14, 10, 2, 2, 2, 1, 1, 1, 3, 4, 4, 4, 13, 18, 65, 65, 65, 65, 65, 1, 1, 45, 45, 45, 32, 32, 14, 14, 14, 10, 10, 2, 3, 3, 4, 13, 13, 65, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 281
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051564 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051564
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051564/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051564
Building REAL300025051565
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051565'
/scratch/stefan/7786831/working/building/REAL300025051565 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051565

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051565/0 /scratch/stefan/7786831/working/building/REAL300025051565 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 437)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/437
`/scratch/stefan/7786831/working/3D/437' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCNC(=O)C1CC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051565.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051565.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051565/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051565 none O=C(CCCNC(=O)C1CC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 5, 6, 8, 8, 8, 8, 29, 29, 1, 1, 1, 4, 7, 7, 7, 26, 45, 129, 129, 129, 129, 129, 1, 1, 5, 5, 7, 7, 8, 7, 8, 29, 29, 29, 29, 29, 2, 4, 4, 7, 26, 26, 129, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 46, 47, 48, 49, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 331
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051565 none O=C(CCCNC(=O)C1CC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 22, 21, 21, 11, 11, 1, 11, 1, 1, 1, 29, 29, 29, 31, 37, 37, 37, 83, 120, 201, 201, 201, 201, 201, 29, 29, 21, 22, 22, 22, 21, 21, 11, 1, 1, 1, 1, 1, 29, 31, 31, 37, 83, 83, 201, 29, 29, 29, 29] 201
rigid atoms, others: [34, 35, 36, 37, 6, 8, 9, 10, 38] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 549
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051565 none O=C(CCCNC(=O)C1CC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [129, 129, 129, 137, 144, 152, 152, 152, 152, 201, 201, 129, 124, 82, 82, 33, 82, 13, 1, 1, 1, 1, 1, 1, 1, 129, 129, 137, 137, 144, 144, 152, 152, 152, 201, 201, 201, 201, 201, 129, 124, 124, 82, 33, 33, 1, 129, 129, 129, 129] 201
rigid atoms, others: [45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49])
total number of confs: 824
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051565 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051565
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051565/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051565
Building REAL300025051566
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051566'
/scratch/stefan/7786831/working/building/REAL300025051566 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051566

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051566/0 /scratch/stefan/7786831/working/building/REAL300025051566 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 438)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/438
`/scratch/stefan/7786831/working/3D/438' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCN1C=CC=CC1=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051566.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051566.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051566/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051566 none O=C(CCN1C=CC=CC1=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 9, 11, 12, 12, 12, 12, 12, 12, 1, 1, 1, 7, 16, 16, 16, 43, 60, 142, 142, 142, 142, 142, 1, 1, 9, 9, 11, 11, 12, 12, 12, 12, 2, 7, 7, 16, 43, 43, 142, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051566 none O=C(CCN1C=CC=CC1=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 31, 52, 52, 52, 111, 136, 201, 201, 201, 201, 201, 12, 12, 5, 5, 3, 3, 1, 1, 1, 1, 12, 31, 31, 52, 111, 111, 201, 12, 12, 12, 12] 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, 43, 44, 45])
total number of confs: 638
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051566 none O=C(CCN1C=CC=CC1=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [142, 142, 142, 201, 201, 201, 201, 201, 201, 201, 201, 142, 111, 53, 53, 27, 53, 13, 1, 1, 1, 1, 1, 1, 1, 142, 142, 201, 201, 201, 201, 201, 201, 201, 201, 142, 111, 111, 53, 27, 27, 1, 142, 142, 142, 142] 201
rigid atoms, others: [41, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 858
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051566 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051566
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051566/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051566
Building REAL300025051567
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051567'
/scratch/stefan/7786831/working/building/REAL300025051567 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051567

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051567/0 /scratch/stefan/7786831/working/building/REAL300025051567 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 439)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/439
`/scratch/stefan/7786831/working/3D/439' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1)

`REAL300025051567.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051567.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051567/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051567 none CCOC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
135  conformations in input
total number of sets (complete confs): 135
using faster count positions algorithm for large data
unique positions, atoms: [13, 8, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 9, 9, 9, 29, 44, 122, 122, 122, 122, 122, 1, 1, 5, 5, 13, 13, 13, 13, 13, 5, 5, 2, 4, 4, 9, 29, 29, 122, 1, 1, 1, 1, 5] 135
rigid atoms, others: [43, 9, 10, 11, 44, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45])
total number of confs: 287
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051567 none CCOC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
135  conformations in input
total number of sets (complete confs): 135
using faster count positions algorithm for large data
unique positions, atoms: [7, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 19, 19, 19, 49, 69, 134, 134, 134, 134, 134, 5, 5, 1, 1, 8, 8, 8, 7, 7, 1, 1, 5, 10, 10, 19, 49, 49, 134, 5, 5, 5, 5, 1] 135
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 45, 25, 26] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 370
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051567 none CCOC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
135  conformations in input
total number of sets (complete confs): 135
using faster count positions algorithm for large data
unique positions, atoms: [135, 135, 134, 134, 134, 134, 122, 122, 122, 122, 103, 75, 75, 36, 75, 13, 1, 1, 1, 1, 1, 1, 1, 122, 122, 134, 134, 135, 135, 135, 135, 135, 134, 134, 122, 103, 103, 75, 36, 36, 1, 122, 122, 122, 122, 134] 135
rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45])
total number of confs: 496
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051567 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051567
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051567/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051567
Building REAL300025051568
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051568'
/scratch/stefan/7786831/working/building/REAL300025051568 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051568

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051568/0 /scratch/stefan/7786831/working/building/REAL300025051568 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 440)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/440
`/scratch/stefan/7786831/working/3D/440' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCC1=O)

`REAL300025051568.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051568.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051568/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051568 none CN1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 2, 2, 2, 1, 1, 1, 6, 20, 20, 20, 48, 57, 146, 147, 147, 147, 147, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 6, 6, 20, 48, 48, 147, 1, 1, 1, 1, 8, 8, 8, 8] 201
rigid atoms, others: [6, 39, 8, 41, 42, 7, 40, 20, 21] set([0, 1, 2, 3, 4, 5, 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, 36, 37, 38, 43, 44, 45, 46])
total number of confs: 353
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051568 none CN1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 8, 8, 26, 61, 61, 61, 115, 129, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 8, 26, 26, 61, 115, 115, 201, 8, 8, 8, 8, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 43, 44, 45, 46, 22, 23, 24, 25, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 622
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051568 none CN1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 147, 147, 147, 147, 93, 51, 51, 29, 51, 13, 1, 1, 1, 1, 1, 1, 1, 147, 147, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 147, 93, 93, 51, 29, 29, 1, 147, 147, 147, 147, 201, 201, 201, 201] 201
rigid atoms, others: [38, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 758
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051568 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051568
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051568/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051568
Building REAL300025051569
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051569'
/scratch/stefan/7786831/working/building/REAL300025051569 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051569

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051569/0 /scratch/stefan/7786831/working/building/REAL300025051569 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 441)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/441
`/scratch/stefan/7786831/working/3D/441' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCCOCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051569.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051569.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051569/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051569 none CCOCCOCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 187, 144, 83, 77, 77, 77, 77, 64, 30, 30, 25, 30, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 201, 201, 201, 201, 201, 201, 201, 187, 187, 83, 83, 77, 64, 64, 30, 25, 25, 1, 77, 77, 77, 77] 201
rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46])
total number of confs: 725
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051569 none CCOCCOCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [74, 70, 45, 28, 10, 3, 2, 2, 2, 1, 1, 1, 4, 15, 15, 15, 30, 32, 77, 77, 77, 77, 77, 1, 1, 74, 74, 74, 74, 74, 45, 45, 28, 28, 3, 3, 2, 4, 4, 15, 30, 30, 77, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 46, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 433
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051569 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051569
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051569/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051569
Building REAL300025051570
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051570'
/scratch/stefan/7786831/working/building/REAL300025051570 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051570

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051570/0 /scratch/stefan/7786831/working/building/REAL300025051570 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 442)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/442
`/scratch/stefan/7786831/working/3D/442' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC(C2CC2)C2CC2)CC1)

`REAL300025051570.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051570.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051570/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051570 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC(C2CC2)C2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 12, 22, 25, 47, 47, 47, 47, 47, 4, 1, 1, 1, 3, 3, 3, 20, 39, 55, 55, 42, 49, 49, 1, 1, 22, 22, 47, 12, 4, 4, 3, 20, 20, 42, 55, 55, 55, 55, 55, 49, 49, 49, 49, 49, 1, 1, 1, 1] 188
rigid atoms, others: [11, 12, 13, 46, 47, 48, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 370
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051570 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC(C2CC2)C2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [31, 19, 12, 1, 1, 1, 1, 1, 1, 1, 31, 31, 45, 47, 47, 47, 47, 150, 184, 188, 188, 187, 187, 187, 47, 47, 19, 19, 1, 31, 45, 45, 47, 150, 150, 187, 188, 188, 188, 188, 188, 187, 187, 187, 187, 187, 47, 47, 47, 47] 188
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 813
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051570 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC(C2CC2)C2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [128, 128, 128, 154, 166, 187, 187, 187, 187, 187, 61, 49, 38, 38, 13, 38, 3, 1, 3, 8, 8, 1, 1, 1, 49, 49, 154, 154, 187, 128, 61, 61, 38, 13, 13, 3, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 49, 49, 49, 49] 188
rigid atoms, others: [41, 42, 43, 44, 45, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48, 49])
total number of confs: 659
number of broken/clashed sets: 1
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051570 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC(C2CC2)C2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [130, 130, 130, 157, 169, 188, 188, 188, 188, 188, 69, 55, 45, 45, 17, 45, 5, 1, 1, 1, 1, 5, 8, 8, 55, 55, 157, 157, 188, 130, 69, 69, 45, 17, 17, 5, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 55, 55, 55, 55] 188
rigid atoms, others: [36, 37, 38, 39, 40, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 671
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051570 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051570
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051570/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051570
Building REAL300025051571
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051571'
/scratch/stefan/7786831/working/building/REAL300025051571 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051571

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051571/0 /scratch/stefan/7786831/working/building/REAL300025051571 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 443)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/443
`/scratch/stefan/7786831/working/3D/443' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CC1)

`REAL300025051571.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051571.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051571/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051571 none CC(CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 191, 105, 105, 105, 105, 87, 53, 53, 25, 53, 13, 1, 1, 1, 1, 1, 1, 1, 105, 105, 201, 201, 201, 201, 201, 201, 201, 191, 191, 105, 87, 87, 53, 25, 25, 1, 105, 105, 105, 105, 201, 201, 201, 201, 201] 201
rigid atoms, others: [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, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 882
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051571 none CC(CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 10, 2, 2, 2, 1, 1, 1, 4, 7, 7, 7, 24, 39, 105, 105, 105, 105, 105, 1, 1, 19, 21, 21, 19, 19, 19, 19, 10, 10, 2, 4, 4, 7, 24, 24, 105, 1, 1, 1, 1, 21, 21, 21, 21, 21] 201
rigid atoms, others: [37, 6, 7, 40, 39, 19, 20, 38, 5] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45])
total number of confs: 300
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051571 none CC(CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 7, 21, 21, 21, 21, 40, 59, 59, 59, 111, 145, 201, 201, 201, 201, 201, 21, 21, 1, 1, 1, 3, 3, 3, 3, 7, 7, 21, 40, 40, 59, 111, 111, 201, 21, 21, 21, 21, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 41, 42, 43, 44, 45, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 645
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051571 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051571
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051571/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051571
Building REAL300025051572
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051572'
/scratch/stefan/7786831/working/building/REAL300025051572 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051572

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051572/0 /scratch/stefan/7786831/working/building/REAL300025051572 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 444)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/444
`/scratch/stefan/7786831/working/3D/444' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C1=CSC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051572.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051572.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051572/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051572 none NC(=O)C1=CSC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 14, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 6, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 4, 5, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 29, 29, 29, 79, 90, 180, 180, 180, 180, 180, 1, 1, 4, 5, 5, 4, 2, 7, 7, 29, 79, 79, 180, 1, 1, 1, 1, 4] 201
rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40])
total number of confs: 471
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051572 none NC(=O)C1=CSC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 14, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 6, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 3, 3, 4, 4, 14, 41, 41, 41, 99, 108, 180, 180, 180, 180, 180, 4, 4, 1, 3, 3, 1, 4, 14, 14, 41, 99, 99, 180, 4, 4, 4, 4, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 25, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 526
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051572 none NC(=O)C1=CSC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 14, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 6, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 180, 201, 180, 180, 180, 180, 180, 180, 180, 117, 48, 48, 28, 48, 12, 1, 1, 1, 1, 1, 1, 1, 180, 180, 180, 201, 201, 180, 180, 117, 117, 48, 28, 28, 1, 180, 180, 180, 180, 180] 201
rigid atoms, others: [35, 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, 36, 37, 38, 39, 40])
total number of confs: 772
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051572 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051572
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051572/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051572
Building REAL300025051573
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051573'
/scratch/stefan/7786831/working/building/REAL300025051573 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051573

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051573/0 /scratch/stefan/7786831/working/building/REAL300025051573 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 445)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/445
`/scratch/stefan/7786831/working/3D/445' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3CCC2CC3)CC1)

`REAL300025051573.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051573.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051573/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051573 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3CCC2CC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 102, 124, 193, 193, 193, 193, 193, 6, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 1, 1, 102, 102, 193, 28, 6, 6, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 46, 47, 48, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 545
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: REAL300025051573 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3CCC2CC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 13, 1, 1, 1, 1, 1, 1, 1, 81, 81, 153, 193, 193, 193, 193, 201, 201, 201, 201, 201, 201, 201, 193, 193, 32, 32, 1, 81, 153, 153, 193, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 193, 193, 193, 193] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 760
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051573 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3CCC2CC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 139, 158, 201, 201, 201, 201, 201, 19, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 139, 139, 201, 57, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 201
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 46, 47, 48, 49])
total number of confs: 644
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051573 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051573
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051573/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051573
Building REAL300025051574
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051574'
/scratch/stefan/7786831/working/building/REAL300025051574 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051574

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051574/0 /scratch/stefan/7786831/working/building/REAL300025051574 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 446)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/446
`/scratch/stefan/7786831/working/3D/446' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CS(C)(=O)=O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051574.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051574.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051574/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051574 none CC(CS(C)(=O)=O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 14, 5, 11, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [197, 173, 197, 198, 201, 201, 201, 173, 173, 173, 139, 71, 71, 30, 71, 13, 1, 1, 1, 1, 1, 1, 1, 173, 173, 197, 197, 197, 197, 198, 198, 201, 201, 201, 173, 139, 139, 71, 30, 30, 1, 173, 173, 173, 173] 201
rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 832
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051574 none CC(CS(C)(=O)=O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 14, 5, 11, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 7, 13, 13, 13, 2, 2, 1, 1, 1, 6, 15, 15, 15, 53, 77, 173, 173, 173, 173, 173, 1, 1, 5, 5, 5, 5, 7, 7, 13, 13, 13, 2, 6, 6, 15, 53, 53, 173, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 434
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051574 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051574
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051574/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051574
Building REAL300025051575
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051575'
/scratch/stefan/7786831/working/building/REAL300025051575 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051575

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051575/0 /scratch/stefan/7786831/working/building/REAL300025051575 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 447)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/447
`/scratch/stefan/7786831/working/3D/447' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C(C)C)

`REAL300025051575.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051575.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051575/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051575 none CCCCC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [198, 198, 194, 186, 116, 116, 116, 116, 103, 81, 81, 30, 81, 13, 1, 1, 1, 1, 1, 1, 1, 116, 116, 186, 193, 197, 198, 198, 198, 198, 198, 198, 198, 194, 194, 186, 116, 103, 103, 81, 30, 30, 1, 116, 116, 116, 116, 197, 197, 197, 197, 197, 197, 197] 201
rigid atoms, others: [42, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 940
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051575 none CCCCC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 15, 13, 8, 2, 2, 2, 1, 1, 1, 4, 7, 7, 7, 25, 49, 116, 116, 116, 116, 116, 1, 1, 8, 14, 15, 18, 18, 18, 18, 18, 15, 15, 13, 13, 8, 2, 4, 4, 7, 25, 25, 116, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15] 201
rigid atoms, others: [7, 8, 9, 43, 44, 45, 46, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 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, 41, 42, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 345
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051575 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051575
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051575/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051575
Building REAL300025051576
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051576'
/scratch/stefan/7786831/working/building/REAL300025051576 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051576

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051576/0 /scratch/stefan/7786831/working/building/REAL300025051576 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 448)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/448
`/scratch/stefan/7786831/working/3D/448' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC(CC(C)C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051576.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051576.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051576/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051576 none CC(C)CC(CC(C)C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 149, 201, 201, 201, 201, 149, 149, 149, 112, 66, 66, 29, 66, 13, 1, 1, 1, 1, 1, 1, 1, 149, 149, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 149, 112, 112, 66, 29, 29, 1, 149, 149, 149, 149] 201
rigid atoms, others: [18, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54, 55, 56])
total number of confs: 861
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: REAL300025051576 none CC(C)CC(CC(C)C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 6, 2, 6, 6, 6, 6, 2, 2, 1, 1, 1, 7, 15, 15, 15, 53, 76, 149, 149, 149, 149, 149, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 7, 7, 15, 53, 53, 149, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 53, 54, 55, 56, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 389
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051576 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051576
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051576/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051576
Building REAL300025051577
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051577'
/scratch/stefan/7786831/working/building/REAL300025051577 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051577

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051577/0 /scratch/stefan/7786831/working/building/REAL300025051577 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 449)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/449
`/scratch/stefan/7786831/working/3D/449' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCC1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051577.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051577.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051577/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051577 none O=C(CCCC1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 10, 14, 17, 36, 36, 36, 36, 1, 1, 1, 4, 6, 6, 6, 17, 23, 52, 52, 52, 52, 52, 1, 1, 10, 10, 17, 17, 17, 17, 36, 36, 36, 36, 36, 36, 36, 36, 36, 2, 4, 4, 6, 17, 17, 52, 1, 1, 1, 1] 201
rigid atoms, others: [10, 11, 12, 48, 49, 50, 51, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025051577 none O=C(CCCC1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [36, 10, 5, 5, 1, 1, 1, 1, 1, 1, 36, 36, 36, 49, 63, 63, 63, 102, 126, 201, 201, 201, 201, 201, 36, 36, 10, 10, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 49, 49, 63, 102, 102, 201, 36, 36, 36, 36] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 39, 40, 36, 38, 37] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 633
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051577 none O=C(CCCC1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [52, 52, 52, 147, 153, 165, 201, 201, 201, 201, 52, 47, 35, 35, 21, 35, 12, 1, 1, 1, 1, 1, 1, 1, 52, 52, 147, 147, 165, 165, 165, 165, 201, 201, 201, 201, 201, 201, 201, 201, 201, 52, 47, 47, 35, 21, 21, 1, 52, 52, 52, 52] 201
rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51])
total number of confs: 889
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051577 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051577
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051577/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051577
Building REAL300025051578
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051578'
/scratch/stefan/7786831/working/building/REAL300025051578 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051578

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051578/0 /scratch/stefan/7786831/working/building/REAL300025051578 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 450)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/450
`/scratch/stefan/7786831/working/3D/450' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N(C)C1=O)

`REAL300025051578.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051578.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051578/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051578 none CN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N(C)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 1, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 2, 2, 2, 1, 1, 1, 6, 21, 21, 21, 57, 69, 163, 163, 163, 163, 163, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 2, 6, 6, 21, 57, 57, 163, 1, 1, 1, 1, 8, 8, 8] 201
rigid atoms, others: [37, 6, 7, 8, 39, 40, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 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, 36, 41, 42, 43])
total number of confs: 395
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: REAL300025051578 none CN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N(C)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 1, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 8, 8, 22, 55, 55, 55, 114, 128, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 2, 2, 2, 1, 8, 22, 22, 55, 114, 114, 201, 8, 8, 8, 8, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 22, 23, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 606
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051578 none CN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N(C)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 1, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 163, 163, 163, 163, 111, 54, 54, 29, 54, 13, 1, 1, 1, 1, 1, 1, 1, 163, 163, 201, 201, 201, 201, 201, 201, 201, 201, 163, 111, 111, 54, 29, 29, 1, 163, 163, 163, 163, 201, 201, 201] 201
rigid atoms, others: [36, 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, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 681
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051578 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051578
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051578/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051578
Building REAL300025051579
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051579'
/scratch/stefan/7786831/working/building/REAL300025051579 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051579

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051579/0 /scratch/stefan/7786831/working/building/REAL300025051579 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 451)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/451
`/scratch/stefan/7786831/working/3D/451' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NSC(C)=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051579.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051579.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051579/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051579 none CC1=NSC(C)=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 4, 20, 20, 20, 69, 84, 142, 142, 142, 142, 142, 1, 1, 7, 7, 7, 7, 7, 7, 2, 4, 4, 20, 69, 69, 142, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 381
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051579 none CC1=NSC(C)=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 15, 70, 70, 70, 141, 160, 201, 201, 201, 201, 201, 7, 7, 2, 2, 2, 2, 2, 2, 7, 15, 15, 70, 141, 141, 201, 7, 7, 7, 7] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 663
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051579 none CC1=NSC(C)=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 142, 142, 142, 142, 115, 62, 62, 26, 62, 13, 1, 1, 1, 1, 1, 1, 1, 142, 142, 201, 201, 201, 201, 201, 201, 142, 115, 115, 62, 26, 26, 1, 142, 142, 142, 142] 201
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41])
total number of confs: 636
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051579 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051579
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051579/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051579
Building REAL300025051580
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051580'
/scratch/stefan/7786831/working/building/REAL300025051580 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051580

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051580/0 /scratch/stefan/7786831/working/building/REAL300025051580 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 452)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/452
`/scratch/stefan/7786831/working/3D/452' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC(C3CC3)=C2)CC1)

`REAL300025051580.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051580.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051580/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051580 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC(C3CC3)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 5, 5, 5, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 31, 37, 76, 76, 76, 76, 76, 4, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 17, 17, 9, 1, 1, 31, 31, 76, 11, 4, 4, 3, 9, 9, 9, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051580 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC(C3CC3)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 5, 5, 5, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [49, 27, 13, 1, 1, 1, 1, 1, 1, 1, 49, 49, 72, 76, 76, 76, 76, 126, 126, 126, 126, 126, 201, 201, 126, 76, 76, 27, 27, 1, 49, 72, 72, 76, 126, 126, 126, 201, 201, 201, 201, 201, 126, 76, 76, 76, 76] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46])
total number of confs: 683
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051580 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC(C3CC3)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 5, 5, 5, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 144, 152, 201, 201, 201, 201, 201, 21, 17, 9, 9, 3, 9, 3, 3, 3, 3, 1, 1, 1, 1, 3, 17, 17, 144, 144, 201, 67, 21, 21, 9, 3, 3, 3, 1, 1, 1, 1, 1, 3, 17, 17, 17, 17] 201
rigid atoms, others: [37, 38, 39, 40, 41, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46])
total number of confs: 673
number of broken/clashed sets: 1
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051580 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC(C3CC3)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 5, 5, 5, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [35, 35, 35, 80, 86, 126, 126, 126, 126, 126, 11, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 3, 1, 9, 9, 80, 80, 126, 35, 11, 11, 5, 1, 1, 1, 3, 3, 3, 3, 3, 1, 9, 9, 9, 9] 201
rigid atoms, others: [34, 35, 36, 42, 14, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 43, 44, 45, 46])
total number of confs: 403
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051580 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051580
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051580/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051580
Building REAL300025051581
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051581'
/scratch/stefan/7786831/working/building/REAL300025051581 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051581

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051581/0 /scratch/stefan/7786831/working/building/REAL300025051581 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 453)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/453
`/scratch/stefan/7786831/working/3D/453' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(C)CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025051581.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051581.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051581/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051581 none CC1CC(C)CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 6, 14, 14, 14, 35, 41, 123, 123, 123, 123, 123, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 6, 6, 14, 35, 35, 123, 1, 1, 1, 1, 7, 7] 201
rigid atoms, others: [9, 10, 11, 46, 47, 48, 49, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51])
total number of confs: 283
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051581 none CC1CC(C)CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 23, 50, 50, 50, 109, 122, 201, 201, 201, 201, 201, 7, 7, 1, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 7, 23, 23, 50, 109, 109, 201, 7, 7, 7, 7, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 50, 37, 51, 25, 38, 36, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 637
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051581 none CC1CC(C)CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 123, 123, 123, 123, 83, 44, 44, 27, 44, 13, 1, 1, 1, 1, 1, 1, 1, 123, 123, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 123, 83, 83, 44, 27, 27, 1, 123, 123, 123, 123, 201, 201] 201
rigid atoms, others: [45, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51])
total number of confs: 727
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051581 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051581
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051581/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051581
Building REAL300025051582
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051582'
/scratch/stefan/7786831/working/building/REAL300025051582 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051582

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051582/0 /scratch/stefan/7786831/working/building/REAL300025051582 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 454)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/454
`/scratch/stefan/7786831/working/3D/454' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1CCC[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051582.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051582.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051582/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051582 none CC(=O)N1CCC[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 7, 7, 2, 7, 2, 2, 1, 1, 1, 7, 23, 23, 23, 61, 77, 156, 156, 156, 156, 156, 1, 1, 9, 9, 9, 7, 7, 7, 7, 7, 7, 2, 7, 7, 23, 61, 61, 156, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
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: REAL300025051582 none CC(=O)N1CCC[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 7, 7, 7, 7, 19, 45, 45, 45, 93, 117, 190, 190, 190, 190, 190, 7, 7, 4, 4, 4, 1, 1, 1, 1, 1, 1, 7, 19, 19, 45, 93, 93, 190, 7, 7, 7, 7] 201
rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 9, 35, 33, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 565
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051582 none CC(=O)N1CCC[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 190, 201, 190, 190, 190, 190, 156, 190, 156, 156, 156, 117, 63, 63, 25, 63, 12, 1, 1, 1, 1, 1, 1, 1, 156, 156, 201, 201, 201, 190, 190, 190, 190, 190, 190, 156, 117, 117, 63, 25, 25, 1, 156, 156, 156, 156] 201
rigid atoms, others: [42, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46])
total number of confs: 743
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051582 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051582
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051582/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051582
Building REAL300025051583
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051583'
/scratch/stefan/7786831/working/building/REAL300025051583 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051583

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051583/0 /scratch/stefan/7786831/working/building/REAL300025051583 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 455)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/455
`/scratch/stefan/7786831/working/3D/455' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1)

`REAL300025051583.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051583.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051583/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051583 none CC(C)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 4, 7, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 24, 24, 24, 74, 86, 198, 198, 198, 198, 198, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 4, 4, 2, 7, 7, 24, 74, 74, 198, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 498
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051583 none CC(C)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 3, 3, 4, 4, 13, 31, 31, 31, 85, 98, 201, 201, 201, 201, 201, 4, 4, 1, 3, 3, 3, 2, 3, 3, 3, 1, 1, 4, 13, 13, 31, 85, 85, 201, 4, 4, 4, 4] 201
rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 7, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 544
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051583 none CC(C)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 198, 198, 198, 126, 44, 44, 27, 44, 12, 1, 1, 1, 1, 1, 1, 1, 198, 198, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 198, 126, 126, 44, 27, 27, 1, 198, 198, 198, 198] 201
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 764
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051583 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051583
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051583/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051583
Building REAL300025051584
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051584'
/scratch/stefan/7786831/working/building/REAL300025051584 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051584

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051584/0 /scratch/stefan/7786831/working/building/REAL300025051584 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 456)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/456
`/scratch/stefan/7786831/working/3D/456' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=C1)

`REAL300025051584.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051584.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051584/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051584 none CN(C)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 4, 7, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 23, 23, 23, 73, 86, 190, 190, 190, 190, 190, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 4, 4, 2, 7, 7, 23, 73, 73, 190, 1, 1, 1, 1, 4] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46])
total number of confs: 477
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051584 none CN(C)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 28, 28, 28, 81, 96, 201, 201, 201, 201, 201, 4, 4, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 4, 11, 11, 28, 81, 81, 201, 4, 4, 4, 4, 1] 201
rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 7, 46, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 514
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051584 none CN(C)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 190, 190, 190, 190, 119, 54, 54, 27, 54, 12, 1, 1, 1, 1, 1, 1, 1, 190, 190, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 190, 119, 119, 54, 27, 27, 1, 190, 190, 190, 190, 201] 201
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46])
total number of confs: 710
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051584 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051584
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051584/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051584
Building REAL300025051585
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051585'
/scratch/stefan/7786831/working/building/REAL300025051585 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051585

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051585/0 /scratch/stefan/7786831/working/building/REAL300025051585 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 457)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/457
`/scratch/stefan/7786831/working/3D/457' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CCCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025051585.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051585.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051585/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051585 none CC1(C)CCCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 6, 14, 14, 14, 36, 41, 106, 106, 106, 106, 106, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 6, 6, 14, 36, 36, 106, 1, 1, 1, 1, 7, 7] 201
rigid atoms, others: [9, 10, 11, 46, 47, 48, 49, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51])
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: REAL300025051585 none CC1(C)CCCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 26, 50, 50, 50, 109, 118, 201, 201, 201, 201, 201, 7, 7, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 26, 26, 50, 109, 109, 201, 7, 7, 7, 7, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 36, 34, 50, 37, 35, 51, 7, 25, 38, 5, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 621
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051585 none CC1(C)CCCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 106, 106, 106, 106, 76, 41, 41, 24, 41, 13, 1, 1, 1, 1, 1, 1, 1, 106, 106, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 106, 76, 76, 41, 24, 24, 1, 106, 106, 106, 106, 201, 201] 201
rigid atoms, others: [45, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51])
total number of confs: 696
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051585 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051585
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051585/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051585
Building REAL300025051586
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051586'
/scratch/stefan/7786831/working/building/REAL300025051586 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051586

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051586/0 /scratch/stefan/7786831/working/building/REAL300025051586 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 458)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/458
`/scratch/stefan/7786831/working/3D/458' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1)

`REAL300025051586.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051586.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051586/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051586 none CC1(C)CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 6, 14, 14, 14, 38, 43, 111, 111, 111, 111, 111, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 6, 6, 14, 38, 38, 111, 1, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [8, 9, 10, 44, 45, 46, 47, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 48, 49, 50, 51])
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: REAL300025051586 none CC1(C)CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 26, 49, 49, 49, 118, 125, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 26, 26, 49, 118, 118, 201, 7, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 48, 49, 50, 51] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 648
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051586 none CC1(C)CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 111, 111, 111, 111, 80, 44, 44, 26, 44, 13, 1, 1, 1, 1, 1, 1, 1, 111, 111, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 111, 80, 80, 44, 26, 26, 1, 111, 111, 111, 111, 201, 201, 201, 201] 201
rigid atoms, others: [43, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 704
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051586 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051586
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051586/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051586
Building REAL300025051587
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051587'
/scratch/stefan/7786831/working/building/REAL300025051587 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051587

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051587/0 /scratch/stefan/7786831/working/building/REAL300025051587 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 459)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/459
`/scratch/stefan/7786831/working/3D/459' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1)

`REAL300025051587.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051587.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051587/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051587 none NC(=O)C1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 6, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 27, 27, 27, 74, 87, 187, 188, 188, 188, 188, 1, 1, 4, 4, 4, 4, 4, 4, 2, 7, 7, 27, 74, 74, 188, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 10, 11, 12, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 463
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051587 none NC(=O)C1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 6, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 15, 50, 50, 50, 111, 123, 201, 201, 201, 201, 201, 4, 4, 1, 2, 2, 1, 1, 1, 4, 15, 15, 50, 111, 111, 201, 4, 4, 4, 4] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 26, 29, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 600
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051587 none NC(=O)C1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 6, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 188, 188, 188, 188, 120, 52, 52, 27, 52, 12, 1, 1, 1, 1, 1, 1, 1, 188, 188, 201, 201, 201, 201, 201, 201, 188, 120, 120, 52, 27, 27, 1, 188, 188, 188, 188] 201
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42])
total number of confs: 734
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051587 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051587
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051587/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051587
Building REAL300025051588
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051588'
/scratch/stefan/7786831/working/building/REAL300025051588 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051588

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051588/0 /scratch/stefan/7786831/working/building/REAL300025051588 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 460)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/460
`/scratch/stefan/7786831/working/3D/460' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(CF)C=C2)CC1)

`REAL300025051588.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051588.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051588/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051588 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(CF)C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 15, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 51, 60, 177, 177, 177, 177, 177, 4, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 25, 5, 5, 1, 1, 51, 51, 177, 13, 4, 4, 3, 5, 5, 25, 25, 5, 5, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
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: REAL300025051588 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(CF)C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 15, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [90, 36, 13, 1, 1, 1, 1, 1, 1, 1, 90, 90, 158, 177, 177, 177, 177, 201, 201, 201, 201, 201, 201, 201, 177, 177, 36, 36, 1, 90, 158, 158, 177, 201, 201, 201, 201, 201, 201, 177, 177, 177, 177] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 718
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051588 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(CF)C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 15, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 25, 82, 92, 201, 201, 201, 201, 201, 7, 5, 3, 3, 1, 3, 1, 1, 1, 1, 1, 8, 1, 1, 5, 5, 82, 82, 201, 25, 7, 7, 3, 1, 1, 8, 8, 1, 1, 5, 5, 5, 5] 201
rigid atoms, others: [33, 34, 37, 38, 14, 16, 17, 18, 19, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 39, 40, 41, 42])
total number of confs: 517
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051588 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051588
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051588/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051588
Building REAL300025051589
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051589'
/scratch/stefan/7786831/working/building/REAL300025051589 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051589

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051589/0 /scratch/stefan/7786831/working/building/REAL300025051589 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 461)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/461
`/scratch/stefan/7786831/working/3D/461' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CCCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051589.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051589.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051589/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051589 none CC1(C)CCCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 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.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 24, 24, 24, 81, 119, 193, 193, 193, 193, 193, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 24, 81, 81, 193, 1, 1, 1, 1] 201
rigid atoms, others: [10, 11, 12, 48, 49, 50, 51, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 508
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051589 none CC1(C)CCCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 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.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 13, 36, 36, 36, 105, 138, 201, 201, 201, 201, 201, 4, 4, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 13, 13, 36, 105, 105, 201, 4, 4, 4, 4] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 7, 8, 39, 34, 40, 35, 32, 36, 38, 37, 5] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 587
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051589 none CC1(C)CCCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 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.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 193, 193, 193, 193, 154, 78, 78, 29, 78, 13, 1, 1, 1, 1, 1, 1, 1, 193, 193, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 193, 154, 154, 78, 29, 29, 1, 193, 193, 193, 193] 201
rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51])
total number of confs: 758
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051589 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051589
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051589/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051589
Building REAL300025051590
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051590'
/scratch/stefan/7786831/working/building/REAL300025051590 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051590

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051590/0 /scratch/stefan/7786831/working/building/REAL300025051590 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 462)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/462
`/scratch/stefan/7786831/working/3D/462' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C12CC(C(=O)NC3(CNC(=O)CSC4=NNC(=O)[N-]4)CC3)(C1)C2)

`REAL300025051590.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051590.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051590/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051590 none CC(C)(C)C12CC(C(=O)NC3(CNC(=O)CSC4=NNC(=O)[N-]4)CC3)(C1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 4, 18, 18, 18, 54, 73, 121, 121, 121, 121, 121, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 4, 4, 18, 54, 54, 121, 1, 1, 1, 1, 7, 7, 7, 7] 144
rigid atoms, others: [9, 10, 11, 45, 46, 47, 48, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52])
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: REAL300025051590 none CC(C)(C)C12CC(C(=O)NC3(CNC(=O)CSC4=NNC(=O)[N-]4)CC3)(C1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 7, 7, 7, 7, 17, 45, 45, 45, 85, 101, 144, 144, 144, 144, 144, 7, 7, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 7, 17, 17, 45, 85, 85, 144, 7, 7, 7, 7, 1, 1, 1, 1] 144
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 50, 49, 37, 51, 52, 25, 26, 27, 28, 29, 36] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 447
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051590 none CC(C)(C)C12CC(C(=O)NC3(CNC(=O)CSC4=NNC(=O)[N-]4)CC3)(C1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [144, 144, 144, 144, 144, 144, 121, 121, 121, 121, 107, 65, 65, 29, 65, 13, 1, 1, 1, 1, 1, 1, 1, 121, 121, 144, 144, 144, 144, 144, 144, 144, 144, 144, 144, 144, 144, 144, 121, 107, 107, 65, 29, 29, 1, 121, 121, 121, 121, 144, 144, 144, 144] 144
rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 489
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051590 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051590
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051590/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051590
Building REAL300025051591
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051591'
/scratch/stefan/7786831/working/building/REAL300025051591 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051591

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051591/0 /scratch/stefan/7786831/working/building/REAL300025051591 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 463)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/463
`/scratch/stefan/7786831/working/3D/463' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@H]2[C@H]3[C@@H]2[C@@H]2CC[C@H]3C2)CC1)

`REAL300025051591.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051591.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051591/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051591 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@H]2[C@H]3[C@@H]2[C@@H]2CC[C@H]3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 7, 5, 7, 5, 7, 5, 5, 5, 7, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 14, 14, 49, 57, 124, 124, 124, 124, 124, 5, 1, 1, 1, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 49, 49, 124, 14, 5, 5, 3, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1] 201
rigid atoms, others: [12, 11, 44, 13, 46, 45, 47, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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])
total number of confs: 338
number of broken/clashed sets: 201
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051591 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@H]2[C@H]3[C@@H]2[C@@H]2CC[C@H]3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 7, 5, 7, 5, 7, 5, 5, 5, 7, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [60, 29, 13, 1, 1, 1, 1, 1, 1, 1, 60, 60, 112, 124, 124, 124, 124, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 124, 124, 29, 29, 1, 60, 112, 112, 124, 201, 201, 201, 201, 201, 201, 124, 124, 124, 124] 201
rigid atoms, others: [33, 3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 728
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051591 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@H]2[C@H]3[C@@H]2[C@@H]2CC[C@H]3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 7, 5, 7, 5, 7, 5, 5, 5, 7, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 136, 141, 201, 201, 201, 201, 201, 31, 22, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 136, 136, 201, 70, 31, 31, 12, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22] 201
rigid atoms, others: [38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47])
total number of confs: 658
number of broken/clashed sets: 201
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051591 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051591
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051591/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051591
Building REAL300025051592
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051592'
/scratch/stefan/7786831/working/building/REAL300025051592 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051592

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051592/0 /scratch/stefan/7786831/working/building/REAL300025051592 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 464)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/464
`/scratch/stefan/7786831/working/3D/464' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1CCCO1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051592.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051592.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051592/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051592 none CC(CC1CCCO1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 2, 7, 11, 16, 16, 16, 16, 2, 2, 1, 1, 1, 5, 9, 9, 9, 31, 48, 136, 136, 136, 136, 136, 1, 1, 7, 7, 7, 7, 11, 11, 16, 16, 16, 16, 16, 16, 16, 2, 5, 5, 9, 31, 31, 136, 1, 1, 1, 1] 201
rigid atoms, others: [10, 11, 12, 46, 47, 48, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
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: REAL300025051592 none CC(CC1CCCO1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 4, 1, 1, 1, 1, 1, 1, 6, 16, 16, 16, 16, 31, 49, 49, 49, 100, 133, 201, 201, 201, 201, 201, 16, 16, 6, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 16, 31, 31, 49, 100, 100, 201, 16, 16, 16, 16] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 35, 36, 38, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 616
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051592 none CC(CC1CCCO1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 136, 201, 201, 201, 201, 201, 201, 136, 136, 136, 125, 69, 69, 28, 69, 13, 1, 1, 1, 1, 1, 1, 1, 136, 136, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 136, 125, 125, 69, 28, 28, 1, 136, 136, 136, 136] 201
rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49])
total number of confs: 856
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051592 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051592
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051592/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051592
Building REAL300025051593
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051593'
/scratch/stefan/7786831/working/building/REAL300025051593 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051593

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051593/0 /scratch/stefan/7786831/working/building/REAL300025051593 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 465)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/465
`/scratch/stefan/7786831/working/3D/465' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CN(C)N=C1)

`REAL300025051593.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051593.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051593/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051593 none COC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CN(C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [141, 140, 100, 100, 100, 100, 85, 52, 52, 27, 52, 13, 1, 1, 1, 1, 1, 1, 1, 100, 100, 140, 201, 201, 201, 201, 201, 141, 141, 141, 140, 100, 85, 85, 52, 27, 27, 1, 100, 100, 100, 100, 201, 201, 201, 201, 201] 201
rigid atoms, others: [37, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 737
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051593 none COC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CN(C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 6, 2, 2, 2, 1, 1, 1, 4, 7, 7, 7, 22, 34, 100, 100, 100, 100, 100, 1, 1, 6, 23, 23, 23, 23, 23, 7, 7, 7, 6, 2, 4, 4, 7, 22, 22, 100, 1, 1, 1, 1, 23, 23, 23, 23, 23] 201
rigid atoms, others: [5, 38, 7, 40, 41, 39, 19, 20, 6] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46])
total number of confs: 240
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051593 none COC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CN(C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 12, 1, 12, 23, 23, 23, 23, 36, 56, 56, 56, 104, 142, 201, 201, 201, 201, 201, 23, 23, 1, 1, 1, 1, 1, 1, 15, 15, 15, 12, 23, 36, 36, 56, 104, 104, 201, 23, 23, 23, 23, 1, 2, 2, 2, 1] 201
rigid atoms, others: [2, 42, 46, 21, 22, 23, 24, 25, 26] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45])
total number of confs: 643
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051593 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051593
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051593/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051593
Building REAL300025051594
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051594'
/scratch/stefan/7786831/working/building/REAL300025051594 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051594

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051594/0 /scratch/stefan/7786831/working/building/REAL300025051594 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 466)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/466
`/scratch/stefan/7786831/working/3D/466' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCOC1)

`REAL300025051594.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051594.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051594/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051594 none COC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 185, 185, 185, 185, 134, 65, 65, 28, 65, 13, 1, 1, 1, 1, 1, 1, 1, 185, 185, 201, 201, 201, 201, 201, 201, 201, 201, 201, 185, 134, 134, 65, 28, 28, 1, 185, 185, 185, 185, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [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, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 756
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051594 none COC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 2, 2, 1, 1, 1, 7, 24, 24, 24, 81, 101, 185, 185, 185, 185, 185, 1, 1, 5, 7, 7, 7, 7, 5, 5, 5, 5, 2, 7, 7, 24, 81, 81, 185, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7] 201
rigid atoms, others: [37, 6, 7, 40, 39, 19, 20, 38, 5] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 503
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051594 none COC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 7, 7, 7, 7, 14, 32, 32, 32, 92, 114, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 5, 5, 5, 4, 7, 14, 14, 32, 92, 92, 201, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [2, 41, 42, 43, 44, 45, 46, 47, 21, 22, 23, 24, 25] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 551
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051594 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051594
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051594/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051594
Building REAL300025051595
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051595'
/scratch/stefan/7786831/working/building/REAL300025051595 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051595

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051595/0 /scratch/stefan/7786831/working/building/REAL300025051595 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 467)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/467
`/scratch/stefan/7786831/working/3D/467' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCCC1)

`REAL300025051595.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051595.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051595/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051595 none CCOC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 128, 128, 128, 128, 92, 56, 56, 26, 56, 13, 1, 1, 1, 1, 1, 1, 1, 128, 128, 148, 201, 201, 201, 201, 148, 148, 148, 148, 148, 148, 128, 92, 92, 56, 26, 26, 1, 128, 128, 128, 128, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [39, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 822
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051595 none CCOC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 2, 2, 2, 1, 1, 1, 7, 17, 17, 17, 52, 60, 128, 128, 128, 128, 128, 1, 1, 4, 7, 7, 7, 7, 4, 4, 4, 4, 4, 4, 2, 7, 7, 17, 52, 52, 128, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] 201
rigid atoms, others: [6, 7, 8, 41, 42, 43, 40, 20, 21] set([0, 1, 2, 3, 4, 5, 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, 36, 37, 38, 39, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 351
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051595 none CCOC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 4, 7, 7, 7, 7, 23, 43, 43, 43, 102, 115, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 7, 23, 23, 43, 102, 102, 201, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [3, 44, 45, 46, 47, 48, 49, 50, 51, 52, 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, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 607
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051595 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051595
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051595/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051595
Building REAL300025051596
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051596'
/scratch/stefan/7786831/working/building/REAL300025051596 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051596

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051596/0 /scratch/stefan/7786831/working/building/REAL300025051596 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 468)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/468
`/scratch/stefan/7786831/working/3D/468' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCOC1)

`REAL300025051596.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051596.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051596/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051596 none CCOC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [194, 194, 194, 159, 159, 159, 159, 127, 81, 81, 30, 81, 13, 1, 1, 1, 1, 1, 1, 1, 159, 159, 194, 201, 201, 201, 201, 194, 194, 194, 194, 194, 194, 159, 127, 127, 81, 30, 30, 1, 159, 159, 159, 159, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [39, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 812
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051596 none CCOC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 6, 2, 2, 2, 1, 1, 1, 6, 15, 15, 15, 52, 85, 159, 159, 159, 159, 159, 1, 1, 6, 9, 9, 9, 9, 7, 7, 7, 7, 7, 6, 2, 6, 6, 15, 52, 52, 159, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9] 201
rigid atoms, others: [6, 7, 8, 41, 42, 43, 40, 20, 21] set([0, 1, 2, 3, 4, 5, 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, 36, 37, 38, 39, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 397
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051596 none CCOC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 4, 9, 9, 9, 9, 20, 34, 34, 34, 81, 121, 201, 201, 201, 201, 201, 9, 9, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 4, 9, 20, 20, 34, 81, 81, 201, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [3, 44, 45, 46, 47, 48, 49, 50, 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, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 535
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051596 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051596
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051596/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051596
Building REAL300025051597
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051597'
/scratch/stefan/7786831/working/building/REAL300025051597 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051597

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051597/0 /scratch/stefan/7786831/working/building/REAL300025051597 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 469)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/469
`/scratch/stefan/7786831/working/3D/469' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CO1)

`REAL300025051597.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051597.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051597/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051597 none COC1=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 2, 2, 2, 2, 2, 2, 1, 1, 1, 7, 23, 23, 23, 78, 84, 201, 201, 201, 201, 201, 1, 1, 2, 2, 4, 4, 4, 2, 7, 7, 23, 78, 78, 201, 1, 1, 1, 1, 2] 201
rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39])
total number of confs: 486
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051597 none COC1=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 2, 2, 2, 2, 7, 23, 23, 23, 78, 84, 201, 201, 201, 201, 201, 2, 2, 1, 1, 4, 4, 4, 2, 7, 7, 23, 78, 78, 201, 2, 2, 2, 2, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 39, 23, 24] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 484
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051597 none COC1=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 119, 53, 53, 30, 53, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 119, 119, 53, 30, 30, 1, 201, 201, 201, 201, 201] 201
rigid atoms, others: [34, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39])
total number of confs: 725
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051597 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051597
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051597/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051597
Building REAL300025051598
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051598'
/scratch/stefan/7786831/working/building/REAL300025051598 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051598

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051598/0 /scratch/stefan/7786831/working/building/REAL300025051598 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 470)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/470
`/scratch/stefan/7786831/working/3D/470' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCC1)

`REAL300025051598.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051598.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051598/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051598 none COC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [196, 196, 179, 179, 179, 179, 119, 64, 64, 28, 64, 13, 1, 1, 1, 1, 1, 1, 1, 179, 179, 196, 201, 201, 201, 196, 196, 196, 196, 179, 119, 119, 64, 28, 28, 1, 179, 179, 179, 179, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 795
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051598 none COC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 6, 2, 2, 2, 1, 1, 1, 7, 18, 18, 18, 62, 87, 179, 179, 179, 179, 179, 1, 1, 6, 11, 11, 11, 7, 7, 7, 6, 2, 7, 7, 18, 62, 62, 179, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11] 201
rigid atoms, others: [36, 5, 6, 7, 39, 19, 20, 38, 37] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 465
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051598 none COC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 4, 1, 4, 11, 11, 11, 11, 24, 39, 39, 39, 94, 123, 201, 201, 201, 201, 201, 11, 11, 1, 1, 1, 1, 6, 6, 6, 4, 11, 24, 24, 39, 94, 94, 201, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [2, 40, 41, 42, 43, 44, 45, 46, 21, 22, 23, 24] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 568
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051598 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051598
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051598/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051598
Building REAL300025051599
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051599'
/scratch/stefan/7786831/working/building/REAL300025051599 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051599

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051599/0 /scratch/stefan/7786831/working/building/REAL300025051599 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 471)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/471
`/scratch/stefan/7786831/working/3D/471' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051599.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051599.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051599/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051599 none CC1=CC=CC(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 21, 21, 21, 21, 11, 9, 2, 2, 2, 1, 1, 1, 5, 12, 12, 12, 31, 47, 103, 103, 103, 103, 103, 1, 1, 21, 21, 21, 21, 21, 21, 21, 11, 11, 9, 9, 2, 5, 5, 12, 31, 31, 103, 1, 1, 1, 1, 21] 201
rigid atoms, others: [44, 10, 11, 12, 45, 46, 47, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48])
total number of confs: 289
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051599 none CC1=CC=CC(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 6, 20, 20, 21, 21, 37, 50, 50, 50, 95, 131, 201, 201, 201, 201, 201, 21, 21, 1, 2, 2, 2, 1, 1, 1, 2, 2, 6, 6, 21, 37, 37, 50, 95, 95, 201, 21, 21, 21, 21, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 48, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 628
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051599 none CC1=CC=CC(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 138, 136, 103, 103, 103, 103, 89, 54, 54, 29, 54, 13, 1, 1, 1, 1, 1, 1, 1, 103, 103, 201, 201, 201, 201, 201, 201, 201, 138, 138, 136, 136, 103, 89, 89, 54, 29, 29, 1, 103, 103, 103, 103, 201] 201
rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48])
total number of confs: 702
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051599 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051599
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051599/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051599
Building REAL300025051600
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051600'
/scratch/stefan/7786831/working/building/REAL300025051600 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051600

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051600/0 /scratch/stefan/7786831/working/building/REAL300025051600 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 472)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/472
`/scratch/stefan/7786831/working/3D/472' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CSN=N2)CC1)

`REAL300025051600.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051600.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051600/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051600 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CSN=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 14, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
128  conformations in input
total number of sets (complete confs): 128
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 38, 70, 124, 124, 124, 124, 124, 5, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 1, 1, 38, 38, 124, 11, 5, 5, 3, 10, 1, 1, 1, 1] 128
rigid atoms, others: [32, 33, 34, 11, 12, 13, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30])
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: REAL300025051600 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CSN=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 14, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
128  conformations in input
total number of sets (complete confs): 128
using faster count positions algorithm for large data
unique positions, atoms: [84, 48, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 113, 124, 126, 126, 126, 128, 128, 128, 128, 124, 124, 48, 48, 1, 84, 113, 113, 126, 128, 124, 124, 124, 124] 128
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 25] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 500
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051600 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CSN=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 14, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
128  conformations in input
total number of sets (complete confs): 128
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 54, 85, 128, 128, 128, 128, 128, 15, 10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 10, 10, 54, 54, 128, 24, 15, 15, 6, 1, 10, 10, 10, 10] 128
rigid atoms, others: [14, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 343
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051600 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051600
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051600/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051600
Building REAL300025051601
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051601'
/scratch/stefan/7786831/working/building/REAL300025051601 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051601

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051601/0 /scratch/stefan/7786831/working/building/REAL300025051601 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 473)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/473
`/scratch/stefan/7786831/working/3D/473' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1)

`REAL300025051601.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051601.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051601/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051601 none CC(C)C1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 3, 8, 3, 3, 2, 2, 2, 1, 1, 1, 7, 27, 27, 27, 76, 91, 187, 187, 187, 187, 187, 1, 1, 3, 3, 8, 8, 8, 8, 8, 8, 8, 3, 2, 7, 7, 27, 76, 76, 187, 1, 1, 1, 1] 201
rigid atoms, others: [43, 8, 9, 10, 23, 44, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
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: REAL300025051601 none CC(C)C1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 2, 2, 3, 3, 10, 32, 32, 32, 84, 99, 191, 191, 191, 191, 191, 3, 3, 1, 1, 5, 5, 5, 4, 5, 5, 5, 1, 3, 10, 10, 32, 84, 84, 191, 3, 3, 3, 3] 201
rigid atoms, others: [1, 3, 4, 5, 6, 33, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 531
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051601 none CC(C)C1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 191, 201, 191, 191, 187, 187, 187, 187, 125, 54, 54, 28, 54, 13, 1, 1, 1, 1, 1, 1, 1, 187, 187, 191, 191, 201, 201, 201, 201, 201, 201, 201, 191, 187, 125, 125, 54, 28, 28, 1, 187, 187, 187, 187] 201
rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 778
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051601 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051601
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051601/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051601
Building REAL300025051602
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051602'
/scratch/stefan/7786831/working/building/REAL300025051602 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051602

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051602/0 /scratch/stefan/7786831/working/building/REAL300025051602 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 474)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/474
`/scratch/stefan/7786831/working/3D/474' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NOC(C3CC3)=C2)CC1)

`REAL300025051602.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051602.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051602/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051602 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NOC(C3CC3)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 5, 5, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 37, 41, 102, 102, 102, 102, 102, 4, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 66, 66, 14, 1, 1, 37, 37, 102, 17, 4, 4, 3, 66, 66, 66, 66, 66, 14, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
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: REAL300025051602 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NOC(C3CC3)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 5, 5, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [48, 31, 13, 1, 1, 1, 1, 1, 1, 1, 48, 48, 79, 102, 102, 102, 102, 138, 138, 138, 138, 201, 201, 138, 102, 102, 31, 31, 1, 48, 79, 79, 102, 201, 201, 201, 201, 201, 138, 102, 102, 102, 102] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 705
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051602 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NOC(C3CC3)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 5, 5, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 153, 153, 187, 189, 201, 201, 201, 201, 201, 85, 66, 53, 53, 12, 53, 12, 12, 12, 1, 1, 1, 1, 12, 66, 66, 187, 187, 201, 153, 85, 85, 53, 1, 1, 1, 1, 1, 12, 66, 66, 66, 66] 201
rigid atoms, others: [33, 34, 35, 36, 37, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42])
total number of confs: 719
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051602 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NOC(C3CC3)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 5, 5, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 56, 56, 86, 87, 138, 138, 138, 138, 138, 19, 14, 10, 9, 1, 9, 1, 1, 1, 1, 1, 12, 12, 1, 14, 14, 86, 86, 138, 56, 19, 19, 10, 12, 12, 12, 12, 12, 1, 14, 14, 14, 14] 201
rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 445
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051602 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051602
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051602/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051602
Building REAL300025051603
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051603'
/scratch/stefan/7786831/working/building/REAL300025051603 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051603

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051603/0 /scratch/stefan/7786831/working/building/REAL300025051603 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 475)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/475
`/scratch/stefan/7786831/working/3D/475' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C)C(C)=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051603.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051603.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051603/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051603 none CC1=NN(C)C(C)=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 12, 2, 2, 2, 1, 1, 1, 6, 15, 15, 15, 43, 62, 132, 132, 132, 132, 132, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 12, 12, 2, 6, 6, 15, 43, 43, 132, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 46, 45, 48, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 354
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: REAL300025051603 none CC1=NN(C)C(C)=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 18, 18, 18, 18, 35, 51, 51, 51, 97, 122, 201, 201, 201, 201, 201, 18, 18, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 18, 35, 35, 51, 97, 97, 201, 18, 18, 18, 18] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 631
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051603 none CC1=NN(C)C(C)=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 184, 132, 132, 132, 132, 109, 63, 63, 27, 63, 12, 1, 1, 1, 1, 1, 1, 1, 132, 132, 201, 201, 201, 201, 201, 201, 201, 201, 201, 184, 184, 132, 109, 109, 63, 27, 27, 1, 132, 132, 132, 132] 201
rigid atoms, others: [44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48])
total number of confs: 796
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051603 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051603
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051603/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051603
Building REAL300025051604
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051604'
/scratch/stefan/7786831/working/building/REAL300025051604 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051604

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051604/0 /scratch/stefan/7786831/working/building/REAL300025051604 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 476)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/476
`/scratch/stefan/7786831/working/3D/476' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=CO2)CC1)

`REAL300025051604.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051604.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051604/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051604 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=CO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 30, 111, 130, 201, 201, 201, 201, 201, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 1, 1, 111, 111, 201, 30, 6, 6, 3, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31])
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: REAL300025051604 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=CO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [78, 32, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 156, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 32, 32, 1, 78, 156, 156, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 25] set([0, 1, 2, 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])
total number of confs: 749
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051604 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=CO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 38, 38, 118, 135, 201, 201, 201, 201, 201, 12, 7, 5, 4, 1, 4, 1, 1, 1, 1, 1, 7, 7, 118, 118, 201, 38, 12, 12, 5, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [14, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35])
total number of confs: 580
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051604 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051604
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051604/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051604
Building REAL300025051605
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051605'
/scratch/stefan/7786831/working/building/REAL300025051605 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051605

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051605/0 /scratch/stefan/7786831/working/building/REAL300025051605 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 477)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/477
`/scratch/stefan/7786831/working/3D/477' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=NC=CC=C23)CC1)

`REAL300025051605.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051605.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051605/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051605 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=NC=CC=C23)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 19, 54, 63, 130, 130, 130, 130, 130, 5, 1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 54, 54, 130, 19, 5, 5, 3, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 42, 11, 12, 13, 44, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
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: REAL300025051605 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=NC=CC=C23)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [57, 29, 13, 1, 1, 1, 1, 1, 1, 1, 57, 57, 106, 130, 130, 130, 130, 201, 201, 201, 201, 201, 201, 201, 201, 201, 130, 130, 29, 29, 1, 57, 106, 106, 130, 201, 201, 201, 201, 201, 201, 130, 130, 130, 130] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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])
total number of confs: 600
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051605 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=NC=CC=C23)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 135, 148, 201, 201, 201, 201, 201, 20, 12, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 135, 135, 201, 64, 20, 20, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12] 201
rigid atoms, others: [35, 36, 37, 38, 39, 40, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44])
total number of confs: 665
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051605 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051605
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051605/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051605
Building REAL300025051606
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051606'
/scratch/stefan/7786831/working/building/REAL300025051606 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051606

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051606/0 /scratch/stefan/7786831/working/building/REAL300025051606 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 478)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/478
`/scratch/stefan/7786831/working/3D/478' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C)C(C)=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051606.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051606.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051606/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051606 none CC1=NN(C)C(C)=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 7, 25, 25, 25, 61, 70, 138, 139, 139, 139, 139, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 7, 7, 25, 61, 61, 139, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 362
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: REAL300025051606 none CC1=NN(C)C(C)=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 7, 7, 7, 7, 23, 58, 58, 58, 113, 124, 201, 201, 201, 201, 201, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 23, 23, 58, 113, 113, 201, 7, 7, 7, 7] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 618
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051606 none CC1=NN(C)C(C)=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 139, 139, 139, 139, 107, 52, 52, 29, 52, 13, 1, 1, 1, 1, 1, 1, 1, 139, 139, 201, 201, 201, 201, 201, 201, 201, 201, 201, 139, 107, 107, 52, 29, 29, 1, 139, 139, 139, 139] 201
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 628
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051606 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051606
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051606/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051606
Building REAL300025051607
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051607'
/scratch/stefan/7786831/working/building/REAL300025051607 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051607

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051607/0 /scratch/stefan/7786831/working/building/REAL300025051607 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 479)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/479
`/scratch/stefan/7786831/working/3D/479' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(C)=C1)

`REAL300025051607.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051607.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051607/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051607 none CC1=NN(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 11, 8, 2, 2, 2, 1, 1, 1, 7, 20, 20, 20, 62, 79, 158, 158, 158, 158, 158, 1, 1, 13, 13, 13, 13, 13, 13, 11, 11, 8, 8, 2, 7, 7, 20, 62, 62, 158, 1, 1, 1, 1, 13, 13, 13, 13] 201
rigid atoms, others: [43, 8, 9, 10, 23, 44, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 45, 46, 47, 48])
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: REAL300025051607 none CC1=NN(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 5, 7, 13, 13, 13, 13, 28, 51, 51, 51, 108, 126, 201, 201, 201, 201, 201, 13, 13, 1, 1, 1, 2, 2, 2, 5, 5, 7, 7, 13, 28, 28, 51, 108, 108, 201, 13, 13, 13, 13, 2, 2, 2, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 48, 24, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 653
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051607 none CC1=NN(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 196, 194, 158, 158, 158, 158, 125, 68, 68, 29, 68, 13, 1, 1, 1, 1, 1, 1, 1, 158, 158, 201, 201, 201, 201, 201, 201, 196, 196, 194, 194, 158, 125, 125, 68, 29, 29, 1, 158, 158, 158, 158, 201, 201, 201, 201] 201
rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 792
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051607 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051607
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051607/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051607
Building REAL300025051608
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051608'
/scratch/stefan/7786831/working/building/REAL300025051608 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051608

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051608/0 /scratch/stefan/7786831/working/building/REAL300025051608 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 480)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/480
`/scratch/stefan/7786831/working/3D/480' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCN1C=CN=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051608.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051608.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051608/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051608 none O=C(CCN1C=CN=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 5, 8, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 8, 12, 25, 25, 25, 25, 1, 1, 1, 5, 13, 13, 13, 34, 51, 106, 106, 106, 106, 106, 1, 1, 8, 8, 12, 12, 25, 25, 25, 2, 5, 5, 13, 34, 34, 106, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 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: REAL300025051608 none O=C(CCN1C=CN=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 5, 8, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 10, 5, 1, 1, 1, 1, 1, 1, 25, 25, 25, 34, 55, 55, 55, 109, 137, 201, 201, 201, 201, 201, 25, 25, 11, 11, 5, 5, 1, 1, 1, 25, 34, 34, 55, 109, 109, 201, 25, 25, 25, 25] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 649
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051608 none O=C(CCN1C=CN=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 5, 8, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [106, 106, 106, 156, 162, 201, 201, 201, 201, 106, 98, 52, 52, 26, 52, 12, 1, 1, 1, 1, 1, 1, 1, 106, 106, 156, 156, 162, 162, 201, 201, 201, 106, 98, 98, 52, 26, 26, 1, 106, 106, 106, 106] 201
rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 788
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051608 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051608
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051608/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051608
Building REAL300025051609
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051609'
/scratch/stefan/7786831/working/building/REAL300025051609 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051609

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051609/0 /scratch/stefan/7786831/working/building/REAL300025051609 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 481)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/481
`/scratch/stefan/7786831/working/3D/481' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(F)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051609.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051609.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051609/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051609 none COC1=CC=C(F)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 5, 5, 5, 2, 5, 5, 5, 2, 2, 2, 1, 1, 1, 7, 20, 20, 20, 58, 69, 152, 152, 152, 152, 152, 1, 1, 7, 7, 7, 5, 4, 5, 2, 7, 7, 20, 58, 58, 152, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 383
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051609 none COC1=CC=C(F)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 17, 42, 42, 42, 101, 112, 201, 201, 201, 201, 201, 5, 5, 4, 4, 4, 1, 1, 1, 5, 17, 17, 42, 101, 101, 201, 5, 5, 5, 5] 201
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: 580
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051609 none COC1=CC=C(F)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 156, 201, 201, 201, 152, 152, 152, 152, 104, 57, 57, 27, 57, 12, 1, 1, 1, 1, 1, 1, 1, 152, 152, 201, 201, 201, 201, 184, 201, 152, 104, 104, 57, 27, 27, 1, 152, 152, 152, 152] 201
rigid atoms, others: [39, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 818
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051609 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051609
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051609/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051609
Building REAL300025051610
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051610'
/scratch/stefan/7786831/working/building/REAL300025051610 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051610

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051610/0 /scratch/stefan/7786831/working/building/REAL300025051610 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 482)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/482
`/scratch/stefan/7786831/working/3D/482' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=C(N2)SC=C3)CC1)

`REAL300025051610.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051610.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051610/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051610 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=C(N2)SC=C3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 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
158  conformations in input
total number of sets (complete confs): 158
using faster count positions algorithm for large data
unique positions, atoms: [28, 28, 28, 77, 89, 148, 148, 148, 148, 148, 6, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 1, 1, 77, 77, 148, 28, 6, 6, 3, 9, 9, 9, 9, 1, 1, 1, 1] 158
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 417
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051610 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=C(N2)SC=C3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 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
158  conformations in input
total number of sets (complete confs): 158
using faster count positions algorithm for large data
unique positions, atoms: [59, 32, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 114, 148, 148, 148, 148, 158, 158, 158, 158, 158, 158, 158, 148, 148, 32, 32, 1, 59, 114, 114, 148, 158, 158, 158, 158, 148, 148, 148, 148] 158
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 565
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051610 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=C(N2)SC=C3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 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
158  conformations in input
total number of sets (complete confs): 158
using faster count positions algorithm for large data
unique positions, atoms: [56, 56, 56, 112, 119, 158, 158, 158, 158, 158, 16, 9, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 112, 112, 158, 56, 16, 16, 6, 1, 1, 1, 1, 9, 9, 9, 9] 158
rigid atoms, others: [33, 34, 35, 36, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40])
total number of confs: 519
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051610 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051610
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051610/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051610
Building REAL300025051611
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051611'
/scratch/stefan/7786831/working/building/REAL300025051611 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051611

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051611/0 /scratch/stefan/7786831/working/building/REAL300025051611 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 483)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/483
`/scratch/stefan/7786831/working/3D/483' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NOC(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1)

`REAL300025051611.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051611.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051611/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051611 none CC1=NOC(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [37, 37, 37, 37, 13, 8, 2, 2, 2, 1, 1, 1, 5, 7, 7, 7, 28, 45, 102, 102, 102, 102, 102, 1, 1, 37, 37, 37, 37, 13, 13, 8, 8, 2, 5, 5, 7, 28, 28, 102, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051611 none CC1=NOC(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 17, 37, 37, 37, 37, 47, 62, 62, 62, 103, 132, 201, 201, 201, 201, 201, 37, 37, 1, 2, 2, 2, 8, 8, 17, 17, 37, 47, 47, 62, 103, 103, 201, 37, 37, 37, 37] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 639
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051611 none CC1=NOC(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 175, 169, 102, 102, 102, 102, 93, 65, 65, 30, 65, 13, 1, 1, 1, 1, 1, 1, 1, 102, 102, 201, 201, 201, 201, 175, 175, 169, 169, 102, 93, 93, 65, 30, 30, 1, 102, 102, 102, 102] 201
rigid atoms, others: [39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 776
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051611 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051611
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051611/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051611
Building REAL300025051612
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051612'
/scratch/stefan/7786831/working/building/REAL300025051612 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051612

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051612/0 /scratch/stefan/7786831/working/building/REAL300025051612 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 484)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/484
`/scratch/stefan/7786831/working/3D/484' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(NC(=O)C(C)(C)C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051612.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051612.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051612/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051612 none CC(NC(=O)C(C)(C)C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [199, 155, 199, 201, 201, 201, 201, 201, 201, 155, 155, 155, 115, 70, 70, 29, 70, 13, 1, 1, 1, 1, 1, 1, 1, 155, 155, 199, 199, 199, 199, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 155, 115, 115, 70, 29, 29, 1, 155, 155, 155, 155] 201
rigid atoms, others: [47, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51])
total number of confs: 808
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051612 none CC(NC(=O)C(C)(C)C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 2, 8, 14, 14, 14, 16, 16, 16, 2, 2, 1, 1, 1, 7, 17, 17, 17, 48, 67, 155, 155, 155, 155, 155, 1, 1, 8, 8, 8, 8, 14, 16, 16, 16, 16, 16, 16, 16, 16, 16, 2, 7, 7, 17, 48, 48, 155, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 48, 49, 50, 51, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 408
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051612 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051612
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051612/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051612
Building REAL300025051613
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051613'
/scratch/stefan/7786831/working/building/REAL300025051613 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051613

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051613/0 /scratch/stefan/7786831/working/building/REAL300025051613 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 485)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/485
`/scratch/stefan/7786831/working/3D/485' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C(=O)NCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051613.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051613.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051613/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051613 none CC(C)(C)C(=O)NCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 189, 116, 116, 116, 116, 93, 56, 56, 28, 56, 13, 1, 1, 1, 1, 1, 1, 1, 116, 116, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 189, 189, 116, 93, 93, 56, 28, 28, 1, 116, 116, 116, 116] 201
rigid atoms, others: [47, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51])
total number of confs: 870
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051613 none CC(C)(C)C(=O)NCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 16, 16, 16, 16, 16, 15, 10, 2, 2, 2, 1, 1, 1, 4, 8, 8, 8, 30, 48, 116, 116, 116, 116, 116, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 15, 15, 10, 10, 2, 4, 4, 8, 30, 30, 116, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 48, 49, 50, 51, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 305
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051613 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051613
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051613/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051613
Building REAL300025051614
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051614'
/scratch/stefan/7786831/working/building/REAL300025051614 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051614

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051614/0 /scratch/stefan/7786831/working/building/REAL300025051614 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 486)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/486
`/scratch/stefan/7786831/working/3D/486' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNC(=O)NCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051614.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051614.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051614/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051614 none CNC(=O)NCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 198, 137, 137, 137, 137, 118, 71, 71, 31, 71, 13, 1, 1, 1, 1, 1, 1, 1, 137, 137, 201, 201, 201, 201, 201, 198, 198, 137, 118, 118, 71, 31, 31, 1, 137, 137, 137, 137] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41])
total number of confs: 854
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051614 none CNC(=O)NCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 16, 16, 16, 12, 2, 2, 2, 1, 1, 1, 6, 13, 13, 13, 38, 55, 137, 137, 137, 137, 137, 1, 1, 20, 20, 20, 20, 16, 12, 12, 2, 6, 6, 13, 38, 38, 137, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 8, 9, 10, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
total number of confs: 358
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051614 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051614
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051614/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051614
Building REAL300025051615
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051615'
/scratch/stefan/7786831/working/building/REAL300025051615 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051615

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051615/0 /scratch/stefan/7786831/working/building/REAL300025051615 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 487)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/487
`/scratch/stefan/7786831/working/3D/487' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCC1CCOCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051615.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051615.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051615/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051615 none O=C(CCCC1CCOCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 10, 14, 15, 33, 33, 33, 33, 33, 1, 1, 1, 3, 5, 5, 5, 15, 23, 57, 57, 57, 57, 57, 1, 1, 10, 10, 15, 15, 15, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 2, 3, 3, 5, 15, 15, 57, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 49, 50, 51, 52, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
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: REAL300025051615 none O=C(CCCC1CCOCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [33, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 41, 52, 52, 52, 97, 127, 201, 201, 201, 201, 201, 33, 33, 9, 9, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 41, 41, 52, 97, 97, 201, 33, 33, 33, 33] 201
rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 39, 40, 41, 36, 38, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 617
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051615 none O=C(CCCC1CCOCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [57, 57, 57, 128, 135, 138, 201, 201, 201, 201, 201, 57, 50, 39, 39, 24, 39, 13, 1, 1, 1, 1, 1, 1, 1, 57, 57, 128, 128, 138, 138, 138, 138, 201, 201, 201, 201, 201, 201, 201, 201, 201, 57, 50, 50, 39, 24, 24, 1, 57, 57, 57, 57] 201
rigid atoms, others: [48, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52])
total number of confs: 823
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051615 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051615
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051615/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051615
Building REAL300025051616
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051616'
/scratch/stefan/7786831/working/building/REAL300025051616 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051616

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051616/0 /scratch/stefan/7786831/working/building/REAL300025051616 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 488)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/488
`/scratch/stefan/7786831/working/3D/488' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC2(CC2C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCO1)

`REAL300025051616.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051616.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051616/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051616 none CC1CC2(CC2C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 6, 6, 2, 2, 2, 1, 1, 1, 6, 21, 21, 21, 54, 62, 134, 134, 134, 134, 134, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 6, 6, 21, 54, 54, 134, 1, 1, 1, 1, 6, 6, 6, 6] 201
rigid atoms, others: [8, 9, 10, 43, 44, 45, 46, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051616 none CC1CC2(CC2C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 19, 63, 63, 63, 130, 140, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 19, 19, 63, 130, 130, 201, 6, 6, 6, 6, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 47, 33, 49, 50, 35, 48, 24, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 626
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051616 none CC1CC2(CC2C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 134, 134, 134, 134, 102, 44, 44, 27, 44, 13, 1, 1, 1, 1, 1, 1, 1, 134, 134, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 134, 102, 102, 44, 27, 27, 1, 134, 134, 134, 134, 201, 201, 201, 201] 201
rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 726
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051616 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051616
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051616/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051616
Building REAL300025051617
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051617'
/scratch/stefan/7786831/working/building/REAL300025051617 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051617

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051617/0 /scratch/stefan/7786831/working/building/REAL300025051617 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 489)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/489
`/scratch/stefan/7786831/working/3D/489' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1C1CC1)

`REAL300025051617.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051617.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051617/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051617 none CN1N=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 5, 5, 5, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 3, 2, 2, 2, 1, 1, 1, 7, 18, 18, 18, 59, 65, 123, 123, 123, 123, 123, 1, 1, 3, 3, 3, 6, 6, 3, 3, 3, 2, 7, 7, 18, 59, 59, 123, 1, 1, 1, 1, 3, 6, 6, 6, 6, 6] 201
rigid atoms, others: [37, 6, 7, 8, 39, 40, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 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, 36, 41, 42, 43, 44, 45, 46])
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: REAL300025051617 none CN1N=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 5, 5, 5, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 3, 9, 20, 20, 20, 60, 66, 123, 123, 123, 123, 123, 3, 3, 1, 1, 1, 5, 5, 2, 2, 2, 3, 9, 9, 20, 60, 60, 123, 3, 3, 3, 3, 1, 5, 5, 5, 5, 5] 201
rigid atoms, others: [0, 1, 2, 3, 4, 41, 22, 23, 24] set([5, 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, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46])
total number of confs: 357
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051617 none CN1N=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 5, 5, 5, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 5, 6, 6, 6, 6, 19, 44, 44, 44, 118, 122, 201, 201, 201, 201, 201, 6, 6, 5, 1, 1, 1, 1, 5, 5, 5, 6, 19, 19, 44, 118, 118, 201, 6, 6, 6, 6, 5, 1, 1, 1, 1, 1] 201
rigid atoms, others: [42, 43, 44, 45, 46, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 609
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051617 none CN1N=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 5, 5, 5, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [123, 123, 123, 123, 123, 123, 123, 81, 44, 44, 27, 44, 13, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 123, 123, 201, 201, 123, 123, 123, 123, 81, 81, 44, 27, 27, 1, 123, 123, 123, 123, 123, 201, 201, 201, 201, 201] 201
rigid atoms, others: [36, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 759
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051617 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051617
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051617/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051617
Building REAL300025051618
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051618'
/scratch/stefan/7786831/working/building/REAL300025051618 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051618

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051618/0 /scratch/stefan/7786831/working/building/REAL300025051618 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 490)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/490
`/scratch/stefan/7786831/working/3D/490' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC3=NNN=C3C=C2)CC1)

`REAL300025051618.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051618.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051618/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051618 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC3=NNN=C3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 8, 8, 8, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 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: [31, 31, 31, 100, 105, 200, 200, 200, 200, 200, 7, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 100, 100, 200, 31, 7, 7, 3, 6, 6, 6, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 540
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051618 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC3=NNN=C3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 8, 8, 8, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 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: [57, 32, 13, 1, 1, 1, 1, 1, 1, 1, 57, 57, 144, 200, 200, 200, 200, 201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 32, 32, 1, 57, 144, 144, 200, 201, 201, 201, 200, 200, 200, 200] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 734
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051618 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC3=NNN=C3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 8, 8, 8, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 48, 134, 137, 201, 201, 201, 201, 201, 12, 6, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 134, 134, 201, 48, 12, 12, 4, 1, 1, 1, 6, 6, 6, 6] 201
rigid atoms, others: [34, 35, 36, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40])
total number of confs: 627
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051618 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051618
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051618/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051618
Building REAL300025051619
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051619'
/scratch/stefan/7786831/working/building/REAL300025051619 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051619

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051619/0 /scratch/stefan/7786831/working/building/REAL300025051619 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 491)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/491
`/scratch/stefan/7786831/working/3D/491' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NN3CCCC3=C2)CC1)

`REAL300025051619.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051619.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051619/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051619 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NN3CCCC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 8, 5, 5, 5, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 31, 31, 108, 118, 201, 201, 201, 201, 201, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 1, 1, 108, 108, 201, 31, 6, 6, 3, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 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: REAL300025051619 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NN3CCCC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 8, 5, 5, 5, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 31, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 154, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 31, 31, 1, 61, 154, 154, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 755
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051619 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NN3CCCC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 8, 5, 5, 5, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [42, 42, 42, 120, 129, 201, 201, 201, 201, 201, 11, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 120, 120, 201, 42, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43])
total number of confs: 585
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051619 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051619
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051619/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051619
Building REAL300025051620
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051620'
/scratch/stefan/7786831/working/building/REAL300025051620 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051620

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051620/0 /scratch/stefan/7786831/working/building/REAL300025051620 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 492)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/492
`/scratch/stefan/7786831/working/3D/492' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)SC=N1)

`REAL300025051620.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051620.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051620/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051620 none CCC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)SC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 4, 4, 2, 2, 2, 1, 1, 1, 7, 16, 16, 16, 69, 98, 192, 192, 192, 192, 192, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 2, 7, 7, 16, 69, 69, 192, 1, 1, 1, 1, 4] 201
rigid atoms, others: [37, 6, 7, 8, 39, 40, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 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, 36, 41])
total number of confs: 496
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051620 none CCC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)SC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 1, 1, 1, 4, 4, 4, 4, 13, 24, 24, 24, 88, 118, 198, 198, 198, 198, 198, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 4, 13, 13, 24, 88, 88, 198, 4, 4, 4, 4, 1] 201
rigid atoms, others: [1, 2, 3, 4, 41, 22, 23, 24] set([0, 5, 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, 36, 37, 38, 39, 40])
total number of confs: 557
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051620 none CCC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)SC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 198, 198, 192, 192, 192, 192, 141, 72, 72, 30, 72, 13, 1, 1, 1, 1, 1, 1, 1, 192, 192, 198, 198, 198, 201, 201, 201, 201, 201, 192, 141, 141, 72, 30, 30, 1, 192, 192, 192, 192, 198] 201
rigid atoms, others: [36, 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, 37, 38, 39, 40, 41])
total number of confs: 756
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051620 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051620
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051620/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051620
Building REAL300025051621
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051621'
/scratch/stefan/7786831/working/building/REAL300025051621 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051621

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051621/0 /scratch/stefan/7786831/working/building/REAL300025051621 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 493)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/493
`/scratch/stefan/7786831/working/3D/493' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=NC(C)=NC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051621.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051621.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051621/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051621 none COC1=NC(C)=NC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 5, 2, 2, 2, 1, 1, 1, 6, 23, 23, 23, 65, 72, 188, 189, 189, 189, 189, 1, 1, 5, 5, 5, 5, 5, 5, 5, 2, 6, 6, 23, 65, 65, 189, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 42, 11, 12, 13, 44, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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])
total number of confs: 434
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051621 none COC1=NC(C)=NC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 53, 53, 53, 117, 122, 201, 201, 201, 201, 201, 5, 5, 2, 2, 2, 2, 2, 2, 1, 5, 14, 14, 53, 117, 117, 201, 5, 5, 5, 5] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 33] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 611
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051621 none COC1=NC(C)=NC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 189, 201, 201, 201, 189, 189, 189, 189, 118, 45, 45, 29, 45, 13, 1, 1, 1, 1, 1, 1, 1, 189, 189, 201, 201, 201, 201, 201, 201, 201, 189, 118, 118, 45, 29, 29, 1, 189, 189, 189, 189] 201
rigid atoms, others: [40, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 804
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051621 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051621
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051621/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051621
Building REAL300025051622
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051622'
/scratch/stefan/7786831/working/building/REAL300025051622 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051622

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051622/0 /scratch/stefan/7786831/working/building/REAL300025051622 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 494)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/494
`/scratch/stefan/7786831/working/3D/494' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCCN3N=C2)CC1)

`REAL300025051622.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051622.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051622/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051622 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCCN3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 77, 97, 167, 167, 167, 167, 167, 6, 1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 1, 1, 77, 77, 167, 22, 6, 6, 3, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 448
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051622 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCCN3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [79, 32, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 140, 167, 167, 167, 167, 201, 201, 201, 201, 201, 201, 201, 167, 167, 32, 32, 1, 79, 140, 140, 167, 201, 201, 201, 201, 201, 201, 201, 167, 167, 167, 167] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 700
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051622 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCCN3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [70, 70, 70, 154, 165, 201, 201, 201, 201, 201, 22, 12, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 154, 154, 201, 70, 22, 22, 7, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43])
total number of confs: 690
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051622 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051622
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051622/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051622
Building REAL300025051623
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051623'
/scratch/stefan/7786831/working/building/REAL300025051623 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051623

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051623/0 /scratch/stefan/7786831/working/building/REAL300025051623 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 495)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/495
`/scratch/stefan/7786831/working/3D/495' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC(F)(F)C2)CC1)

`REAL300025051623.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051623.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051623/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051623 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC(F)(F)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', '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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 19, 57, 72, 147, 147, 147, 147, 147, 5, 1, 1, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 1, 1, 57, 57, 147, 19, 5, 5, 3, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 382
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051623 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC(F)(F)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', '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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [69, 31, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 123, 147, 147, 147, 147, 201, 201, 201, 201, 201, 201, 147, 147, 31, 31, 1, 69, 123, 123, 147, 201, 201, 201, 201, 201, 201, 201, 147, 147, 147, 147] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 739
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051623 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC(F)(F)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', '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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [73, 73, 73, 142, 159, 201, 201, 201, 201, 201, 22, 17, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 17, 17, 142, 142, 201, 73, 22, 22, 9, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42])
total number of confs: 656
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051623 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051623
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051623/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051623
Building REAL300025051624
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051624'
/scratch/stefan/7786831/working/building/REAL300025051624 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051624

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051624/0 /scratch/stefan/7786831/working/building/REAL300025051624 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 496)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/496
`/scratch/stefan/7786831/working/3D/496' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CN=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(F)=C1)

`REAL300025051624.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051624.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051624/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051624 none COC1=CN=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 26, 26, 26, 74, 85, 192, 192, 192, 192, 192, 1, 1, 4, 4, 4, 6, 6, 6, 4, 2, 7, 7, 26, 74, 74, 192, 1, 1, 1, 1, 4] 201
rigid atoms, others: [38, 39, 8, 9, 10, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 42])
total number of confs: 464
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051624 none COC1=CN=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 14, 38, 38, 38, 91, 103, 201, 201, 201, 201, 201, 4, 4, 1, 1, 1, 3, 3, 3, 1, 4, 14, 14, 38, 91, 91, 201, 4, 4, 4, 4, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 42, 24, 25, 26, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 529
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051624 none COC1=CN=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 192, 192, 192, 192, 119, 48, 48, 28, 48, 13, 1, 1, 1, 1, 1, 1, 1, 192, 192, 201, 201, 201, 201, 201, 201, 201, 192, 119, 119, 48, 28, 28, 1, 192, 192, 192, 192, 201] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 726
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051624 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051624
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051624/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051624
Building REAL300025051625
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051625'
/scratch/stefan/7786831/working/building/REAL300025051625 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051625

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051625/0 /scratch/stefan/7786831/working/building/REAL300025051625 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 497)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/497
`/scratch/stefan/7786831/working/3D/497' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)N1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=N1)

`REAL300025051625.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051625.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051625/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051625 none CC(C)(C)N1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 3, 7, 7, 3, 3, 2, 2, 2, 1, 1, 1, 7, 25, 25, 25, 65, 83, 200, 200, 200, 200, 200, 1, 1, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 2, 7, 7, 25, 65, 65, 200, 1, 1, 1, 1] 201
rigid atoms, others: [9, 10, 11, 44, 45, 46, 47, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 485
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051625 none CC(C)(C)N1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 3, 10, 31, 31, 31, 76, 98, 201, 201, 201, 201, 201, 3, 3, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 3, 10, 10, 31, 76, 76, 201, 3, 3, 3, 3] 201
rigid atoms, others: [1, 4, 5, 6, 7, 25, 36, 26] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 510
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051625 none CC(C)(C)N1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 200, 200, 200, 200, 132, 68, 68, 29, 68, 13, 1, 1, 1, 1, 1, 1, 1, 200, 200, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 132, 132, 68, 29, 29, 1, 200, 200, 200, 200] 201
rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47])
total number of confs: 737
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051625 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051625
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051625/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051625
Building REAL300025051626
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051626'
/scratch/stefan/7786831/working/building/REAL300025051626 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051626

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051626/0 /scratch/stefan/7786831/working/building/REAL300025051626 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 498)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/498
`/scratch/stefan/7786831/working/3D/498' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CNC=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051626.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051626.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051626/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051626 none O=C(CCC1=CNC=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 5, 1, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 8, 13, 15, 15, 15, 15, 1, 1, 1, 5, 12, 12, 12, 44, 75, 171, 171, 171, 171, 171, 1, 1, 8, 8, 13, 13, 15, 15, 15, 2, 5, 5, 12, 44, 44, 171, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 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: REAL300025051626 none O=C(CCC1=CNC=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 5, 1, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 10, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 22, 36, 36, 36, 86, 127, 201, 201, 201, 201, 201, 15, 15, 10, 10, 6, 6, 1, 1, 1, 15, 22, 22, 36, 86, 86, 201, 15, 15, 15, 15] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 562
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051626 none O=C(CCC1=CNC=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 5, 1, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [171, 171, 171, 201, 201, 201, 201, 201, 201, 171, 150, 105, 105, 35, 105, 13, 1, 1, 1, 1, 1, 1, 1, 171, 171, 201, 201, 201, 201, 201, 201, 201, 171, 150, 150, 105, 35, 35, 1, 171, 171, 171, 171] 201
rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 795
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051626 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051626/1 /scratch/stefan/7786831/working/building/REAL300025051626 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 499)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/499
`/scratch/stefan/7786831/working/3D/499' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CN=CN1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051626.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051626.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051626/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051626 none O=C(CCC1=CN=CN1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 5, 1, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
183  conformations in input
total number of sets (complete confs): 183
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 9, 15, 16, 16, 16, 16, 1, 1, 1, 7, 18, 18, 18, 43, 63, 136, 136, 136, 136, 136, 1, 1, 9, 9, 15, 15, 16, 16, 16, 2, 7, 7, 18, 43, 43, 136, 1, 1, 1, 1] 183
rigid atoms, others: [39, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 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: REAL300025051626 none O=C(CCC1=CN=CN1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 5, 1, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
183  conformations in input
total number of sets (complete confs): 183
using faster count positions algorithm for large data
unique positions, atoms: [16, 6, 3, 1, 1, 1, 1, 1, 1, 16, 16, 16, 30, 49, 49, 49, 96, 126, 183, 183, 183, 183, 183, 16, 16, 6, 6, 3, 3, 1, 1, 1, 16, 30, 30, 49, 96, 96, 183, 16, 16, 16, 16] 183
rigid atoms, others: [3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 576
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051626 none O=C(CCC1=CN=CN1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 5, 1, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
183  conformations in input
total number of sets (complete confs): 183
using faster count positions algorithm for large data
unique positions, atoms: [136, 136, 136, 175, 183, 183, 183, 183, 183, 136, 103, 54, 54, 28, 54, 13, 1, 1, 1, 1, 1, 1, 1, 136, 136, 175, 175, 183, 183, 183, 183, 183, 136, 103, 103, 54, 28, 28, 1, 136, 136, 136, 136] 183
rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 771
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051626 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051626
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051626/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051626/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051626
Building REAL300025051627
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051627'
/scratch/stefan/7786831/working/building/REAL300025051627 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051627

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051627/0 /scratch/stefan/7786831/working/building/REAL300025051627 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 500)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/500
`/scratch/stefan/7786831/working/3D/500' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCC(F)(F)C2)CC1)

`REAL300025051627.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051627.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051627/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051627 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCC(F)(F)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 15, 15, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 16, 20, 56, 56, 56, 56, 56, 5, 1, 1, 1, 3, 3, 3, 18, 49, 49, 49, 49, 49, 49, 1, 1, 16, 16, 56, 10, 5, 5, 3, 18, 18, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
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: REAL300025051627 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCC(F)(F)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 15, 15, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [37, 27, 13, 1, 1, 1, 1, 1, 1, 1, 37, 37, 54, 56, 56, 56, 56, 175, 201, 201, 201, 201, 201, 201, 56, 56, 27, 27, 1, 37, 54, 54, 56, 175, 175, 201, 201, 201, 201, 201, 201, 201, 56, 56, 56, 56] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 796
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051627 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCC(F)(F)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 15, 15, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [99, 99, 99, 128, 151, 201, 201, 201, 201, 201, 53, 49, 30, 30, 6, 30, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 128, 128, 201, 99, 53, 53, 30, 6, 6, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49] 201
rigid atoms, others: [35, 36, 37, 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, 42, 43, 44, 45])
total number of confs: 636
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051627 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051627
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051627/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051627
Building REAL300025051628
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051628'
/scratch/stefan/7786831/working/building/REAL300025051628 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051628

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051628/0 /scratch/stefan/7786831/working/building/REAL300025051628 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 501)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/501
`/scratch/stefan/7786831/working/3D/501' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(C(F)F)N=C2)CC1)

`REAL300025051628.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051628.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051628/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051628 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(C(F)F)N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 15, 15, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 53, 65, 144, 144, 144, 144, 144, 6, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 26, 26, 9, 9, 1, 1, 53, 53, 144, 16, 6, 6, 3, 9, 9, 26, 9, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 421
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051628 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(C(F)F)N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 15, 15, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 34, 13, 1, 1, 1, 1, 1, 1, 1, 81, 81, 126, 144, 144, 144, 144, 201, 201, 201, 201, 201, 201, 201, 201, 144, 144, 34, 34, 1, 81, 126, 126, 144, 201, 201, 201, 201, 144, 144, 144, 144] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 637
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051628 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(C(F)F)N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 15, 15, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [37, 37, 37, 108, 124, 201, 201, 201, 201, 201, 16, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 6, 6, 1, 1, 9, 9, 108, 108, 201, 37, 16, 16, 5, 1, 1, 6, 1, 9, 9, 9, 9] 201
rigid atoms, others: [34, 35, 37, 14, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 38, 39, 40, 41])
total number of confs: 602
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051628 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051628
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051628/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051628
Building REAL300025051629
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051629'
/scratch/stefan/7786831/working/building/REAL300025051629 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051629

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051629/0 /scratch/stefan/7786831/working/building/REAL300025051629 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 502)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/502
`/scratch/stefan/7786831/working/3D/502' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCN1C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051629.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051629.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051629/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051629 none C=CCN1C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [1, 1, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 9, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 4, 8, 8, 8, 27, 38, 125, 125, 125, 125, 125, 1, 1, 21, 21, 21, 9, 9, 4, 4, 4, 2, 4, 4, 8, 27, 27, 125, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 10, 11, 12, 44, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 300
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051629 none C=CCN1C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [1, 1, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 8, 16, 16, 16, 48, 66, 175, 175, 175, 175, 175, 4, 4, 13, 13, 13, 5, 5, 1, 1, 1, 4, 8, 8, 16, 48, 48, 175, 4, 4, 4, 4] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 421
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051629 none C=CCN1C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [1, 1, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 175, 175, 175, 175, 175, 125, 125, 125, 125, 101, 64, 64, 27, 64, 12, 1, 1, 1, 1, 1, 1, 1, 125, 125, 201, 201, 201, 201, 201, 175, 175, 175, 125, 101, 101, 64, 27, 27, 1, 125, 125, 125, 125] 201
rigid atoms, others: [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, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 746
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051629 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051629
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051629/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051629
Building REAL300025051630
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051630'
/scratch/stefan/7786831/working/building/REAL300025051630 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051630

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051630/0 /scratch/stefan/7786831/working/building/REAL300025051630 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 503)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/503
`/scratch/stefan/7786831/working/3D/503' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@H+](CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCC1)

`REAL300025051630.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051630.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051630/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051630 none C[N@H+](CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 25, 25, 19, 25, 12, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 25, 19, 19, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 28
rigid atoms, others: [37, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
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: REAL300025051630 none C[N@H+](CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [4, 3, 4, 2, 2, 2, 1, 1, 1, 3, 5, 5, 5, 10, 14, 28, 28, 28, 28, 28, 1, 1, 4, 6, 6, 6, 4, 4, 4, 3, 3, 2, 3, 3, 5, 10, 10, 28, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6] 28
rigid atoms, others: [6, 38, 7, 8, 41, 39, 40, 20, 21] set([0, 1, 2, 3, 4, 5, 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, 36, 37, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 93
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051630 none C[N@H+](CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 4, 6, 6, 6, 6, 7, 8, 8, 8, 14, 17, 28, 28, 28, 28, 28, 6, 6, 1, 1, 1, 1, 2, 2, 2, 4, 4, 6, 7, 7, 8, 14, 14, 28, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1] 28
rigid atoms, others: [1, 42, 43, 44, 45, 46, 47, 48, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 94
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051630 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051630/1 /scratch/stefan/7786831/working/building/REAL300025051630 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 504)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/504
`/scratch/stefan/7786831/working/3D/504' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@@H+](CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCC1)

`REAL300025051630.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051630.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051630/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051630 none C[N@@H+](CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 26, 26, 19, 26, 12, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 26, 19, 19, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 29
rigid atoms, others: [37, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
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: REAL300025051630 none C[N@@H+](CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [4, 3, 4, 2, 2, 2, 1, 1, 1, 3, 5, 5, 5, 10, 14, 29, 29, 29, 29, 29, 1, 1, 4, 7, 7, 7, 4, 4, 4, 3, 3, 2, 3, 3, 5, 10, 10, 29, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7] 29
rigid atoms, others: [6, 38, 7, 8, 41, 39, 40, 20, 21] set([0, 1, 2, 3, 4, 5, 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, 36, 37, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 98
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051630 none C[N@@H+](CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 3, 5, 7, 7, 7, 7, 8, 10, 10, 10, 16, 18, 29, 29, 29, 29, 29, 7, 7, 1, 1, 1, 1, 3, 3, 3, 5, 5, 7, 8, 8, 10, 16, 16, 29, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1] 29
rigid atoms, others: [1, 42, 43, 44, 45, 46, 47, 48, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 100
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051630 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051630
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051630/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051630/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051630
Building REAL300025051631
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051631'
/scratch/stefan/7786831/working/building/REAL300025051631 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051631

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051631/0 /scratch/stefan/7786831/working/building/REAL300025051631 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 505)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/505
`/scratch/stefan/7786831/working/3D/505' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3C=NC=CN3N=C2)CC1)

`REAL300025051631.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051631.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051631/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051631 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3C=NC=CN3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 26, 26, 95, 112, 194, 194, 194, 194, 194, 6, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 95, 95, 194, 26, 6, 6, 3, 8, 8, 8, 8, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 511
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051631 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3C=NC=CN3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [72, 32, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 138, 194, 194, 194, 194, 201, 201, 201, 201, 201, 201, 201, 201, 194, 194, 32, 32, 1, 72, 138, 138, 194, 201, 201, 201, 201, 194, 194, 194, 194] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 715
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051631 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3C=NC=CN3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [60, 60, 60, 142, 153, 201, 201, 201, 201, 201, 16, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 142, 142, 201, 60, 16, 16, 5, 1, 1, 1, 1, 8, 8, 8, 8] 201
rigid atoms, others: [34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 644
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051631 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051631
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051631/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051631
Building REAL300025051632
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051632'
/scratch/stefan/7786831/working/building/REAL300025051632 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051632

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051632/0 /scratch/stefan/7786831/working/building/REAL300025051632 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 506)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/506
`/scratch/stefan/7786831/working/3D/506' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NN3CCOC3=C2)CC1)

`REAL300025051632.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051632.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051632/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051632 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NN3CCOC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 8, 5, 5, 12, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 31, 31, 112, 121, 201, 201, 201, 201, 201, 6, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 1, 1, 112, 112, 201, 31, 6, 6, 3, 6, 6, 6, 6, 6, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 570
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051632 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NN3CCOC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 8, 5, 5, 12, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 31, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 153, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 31, 31, 1, 65, 153, 153, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 744
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051632 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NN3CCOC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 8, 5, 5, 12, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [41, 41, 41, 125, 132, 201, 201, 201, 201, 201, 10, 6, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 125, 125, 201, 41, 10, 10, 4, 1, 1, 1, 1, 1, 6, 6, 6, 6] 201
rigid atoms, others: [33, 34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41])
total number of confs: 597
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051632 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051632
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051632/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051632
Building REAL300025051633
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051633'
/scratch/stefan/7786831/working/building/REAL300025051633 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051633

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051633/0 /scratch/stefan/7786831/working/building/REAL300025051633 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 507)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/507
`/scratch/stefan/7786831/working/3D/507' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2CCOCC2=O)CC1)

`REAL300025051633.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051633.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051633/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051633 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2CCOCC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 5, 5, 12, 5, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [10, 10, 10, 17, 19, 50, 50, 50, 50, 50, 4, 1, 1, 1, 3, 3, 3, 21, 33, 33, 33, 33, 33, 33, 1, 1, 17, 17, 50, 10, 4, 4, 3, 21, 21, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1] 91
rigid atoms, others: [43, 41, 42, 11, 12, 13, 44, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 200
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051633 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2CCOCC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 5, 5, 12, 5, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [32, 22, 12, 1, 1, 1, 1, 1, 1, 1, 32, 32, 47, 50, 50, 50, 50, 87, 91, 91, 91, 91, 91, 91, 50, 50, 22, 22, 1, 32, 47, 47, 50, 87, 87, 91, 91, 91, 91, 91, 91, 50, 50, 50, 50] 91
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 378
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051633 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2CCOCC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 5, 5, 12, 5, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [60, 60, 60, 70, 72, 91, 91, 91, 91, 91, 37, 33, 31, 30, 7, 30, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 70, 70, 91, 60, 37, 37, 31, 7, 7, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33] 91
rigid atoms, others: [35, 36, 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, 41, 42, 43, 44])
total number of confs: 275
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051633 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051633
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051633/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051633
Building REAL300025051634
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051634'
/scratch/stefan/7786831/working/building/REAL300025051634 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051634

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051634/0 /scratch/stefan/7786831/working/building/REAL300025051634 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 508)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/508
`/scratch/stefan/7786831/working/3D/508' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=NNN=C3N=C2)CC1)

`REAL300025051634.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051634.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051634/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051634 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=NNN=C3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 8, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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: [24, 24, 24, 71, 80, 128, 128, 128, 128, 128, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 71, 71, 128, 24, 5, 5, 3, 9, 9, 9, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051634 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=NNN=C3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 8, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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: [57, 26, 13, 1, 1, 1, 1, 1, 1, 1, 57, 57, 99, 128, 128, 128, 128, 201, 201, 201, 201, 201, 201, 201, 201, 128, 128, 26, 26, 1, 57, 99, 99, 128, 201, 201, 201, 128, 128, 128, 128] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 601
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051634 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=NNN=C3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 8, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 61, 61, 147, 157, 201, 201, 201, 201, 201, 14, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 147, 147, 201, 61, 14, 14, 5, 1, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [34, 35, 36, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40])
total number of confs: 666
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051634 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051634
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051634/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051634
Building REAL300025051635
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051635'
/scratch/stefan/7786831/working/building/REAL300025051635 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051635

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051635/0 /scratch/stefan/7786831/working/building/REAL300025051635 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 509)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/509
`/scratch/stefan/7786831/working/3D/509' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1)

`REAL300025051635.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051635.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051635/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051635 none CCC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 21, 21, 21, 54, 58, 121, 121, 121, 121, 121, 1, 1, 4, 9, 9, 9, 9, 9, 4, 4, 4, 2, 7, 7, 21, 54, 54, 121, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
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: REAL300025051635 none CCC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 25, 25, 25, 61, 65, 122, 122, 122, 122, 122, 4, 4, 1, 6, 6, 6, 6, 6, 1, 1, 1, 4, 10, 10, 25, 61, 61, 122, 4, 4, 4, 4] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 25, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 365
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051635 none CCC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 122, 122, 122, 122, 122, 121, 121, 121, 121, 77, 37, 37, 21, 37, 12, 1, 1, 1, 1, 1, 1, 1, 121, 121, 122, 201, 201, 201, 201, 201, 122, 122, 122, 121, 77, 77, 37, 21, 21, 1, 121, 121, 121, 121] 201
rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 921
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051635 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051635
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051635/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051635
Building REAL300025051636
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051636'
/scratch/stefan/7786831/working/building/REAL300025051636 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051636

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051636/0 /scratch/stefan/7786831/working/building/REAL300025051636 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 510)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/510
`/scratch/stefan/7786831/working/3D/510' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3C=CC=NN3N=C2)CC1)

`REAL300025051636.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051636.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051636/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051636 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3C=CC=NN3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 26, 26, 78, 100, 179, 179, 179, 179, 179, 6, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 78, 78, 179, 26, 6, 6, 3, 14, 14, 14, 14, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 459
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051636 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3C=CC=NN3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [66, 31, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 135, 179, 179, 179, 179, 201, 201, 201, 201, 201, 201, 201, 201, 179, 179, 31, 31, 1, 66, 135, 135, 179, 201, 201, 201, 201, 179, 179, 179, 179] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 700
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051636 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3C=CC=NN3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [78, 78, 78, 143, 153, 201, 201, 201, 201, 201, 23, 14, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 143, 143, 201, 78, 23, 23, 9, 1, 1, 1, 1, 14, 14, 14, 14] 201
rigid atoms, others: [34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 661
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051636 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051636
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051636/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051636
Building REAL300025051637
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051637'
/scratch/stefan/7786831/working/building/REAL300025051637 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051637

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051637/0 /scratch/stefan/7786831/working/building/REAL300025051637 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 511)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/511
`/scratch/stefan/7786831/working/3D/511' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C)C=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051637.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051637.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051637/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051637 none CC1=NN(C)C=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 24, 24, 24, 12, 2, 2, 2, 1, 1, 1, 5, 10, 10, 10, 34, 51, 130, 130, 130, 130, 130, 1, 1, 24, 24, 24, 24, 24, 24, 24, 12, 12, 2, 5, 5, 10, 34, 34, 130, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 335
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051637 none CC1=NN(C)C=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 24, 24, 24, 24, 36, 46, 46, 46, 93, 118, 201, 201, 201, 201, 201, 24, 24, 2, 2, 2, 2, 2, 2, 1, 5, 5, 24, 36, 36, 46, 93, 93, 201, 24, 24, 24, 24] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 614
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051637 none CC1=NN(C)C=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 181, 130, 130, 130, 130, 111, 71, 71, 30, 71, 13, 1, 1, 1, 1, 1, 1, 1, 130, 130, 201, 201, 201, 201, 201, 201, 201, 181, 181, 130, 111, 111, 71, 30, 30, 1, 130, 130, 130, 130] 201
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 783
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051637 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051637
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051637/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051637
Building REAL300025051638
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051638'
/scratch/stefan/7786831/working/building/REAL300025051638 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051638

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051638/0 /scratch/stefan/7786831/working/building/REAL300025051638 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 512)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/512
`/scratch/stefan/7786831/working/3D/512' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C)=CN=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051638.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051638.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051638/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051638 none COC1=CC(C)=CN=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 6, 18, 18, 18, 59, 81, 193, 193, 193, 193, 193, 1, 1, 13, 13, 13, 7, 7, 7, 7, 7, 2, 6, 6, 18, 59, 59, 193, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 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: REAL300025051638 none COC1=CC(C)=CN=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 18, 35, 35, 35, 89, 109, 201, 201, 201, 201, 201, 7, 7, 4, 4, 4, 1, 2, 2, 2, 1, 7, 18, 18, 35, 89, 89, 201, 7, 7, 7, 7] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 30] set([0, 10, 11, 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])
total number of confs: 548
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051638 none COC1=CC(C)=CN=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 193, 193, 193, 193, 137, 68, 68, 30, 68, 13, 1, 1, 1, 1, 1, 1, 1, 193, 193, 201, 201, 201, 201, 201, 201, 201, 201, 193, 137, 137, 68, 30, 30, 1, 193, 193, 193, 193] 201
rigid atoms, others: [41, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 747
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051638 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051638
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051638/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051638
Building REAL300025051639
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051639'
/scratch/stefan/7786831/working/building/REAL300025051639 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051639

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051639/0 /scratch/stefan/7786831/working/building/REAL300025051639 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 513)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/513
`/scratch/stefan/7786831/working/3D/513' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(F)C=N2)CC1)

`REAL300025051639.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051639.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051639/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051639 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(F)C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 31, 31, 102, 113, 201, 201, 201, 201, 201, 6, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 1, 1, 102, 102, 201, 31, 6, 6, 3, 6, 6, 6, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 548
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051639 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(F)C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 31, 13, 1, 1, 1, 1, 1, 1, 1, 63, 63, 148, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 31, 31, 1, 63, 148, 148, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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])
total number of confs: 744
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051639 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(F)C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [49, 49, 49, 129, 138, 201, 201, 201, 201, 201, 11, 6, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 129, 129, 201, 49, 11, 11, 4, 1, 1, 1, 6, 6, 6, 6] 201
rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38])
total number of confs: 617
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051639 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051639
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051639/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051639
Building REAL300025051640
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051640'
/scratch/stefan/7786831/working/building/REAL300025051640 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051640

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051640/0 /scratch/stefan/7786831/working/building/REAL300025051640 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 514)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/514
`/scratch/stefan/7786831/working/3D/514' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCCCCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051640.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051640.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051640/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051640 none CCOCCCCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 200, 147, 153, 147, 138, 64, 64, 64, 64, 60, 48, 48, 40, 48, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 201, 201, 201, 201, 201, 195, 201, 153, 153, 153, 153, 153, 153, 138, 138, 64, 60, 60, 48, 40, 40, 1, 64, 64, 64, 64] 201
rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51])
total number of confs: 949
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051640 none CCOCCCCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 32, 29, 12, 13, 12, 10, 2, 2, 2, 1, 1, 1, 3, 5, 5, 5, 18, 27, 64, 64, 64, 64, 64, 1, 1, 32, 32, 32, 32, 32, 29, 30, 13, 13, 13, 13, 13, 13, 10, 10, 2, 3, 3, 5, 18, 18, 64, 1, 1, 1, 1] 201
rigid atoms, others: [10, 11, 12, 48, 49, 50, 51, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 284
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051640 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051640
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051640/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051640
Building REAL300025051641
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051641'
/scratch/stefan/7786831/working/building/REAL300025051641 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051641

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051641/0 /scratch/stefan/7786831/working/building/REAL300025051641 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 515)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/515
`/scratch/stefan/7786831/working/3D/515' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNC(=O)CCCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051641.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051641.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051641/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051641 none CNC(=O)CCCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 200, 201, 185, 181, 176, 111, 111, 111, 111, 92, 82, 82, 32, 82, 13, 1, 1, 1, 1, 1, 1, 1, 111, 111, 201, 201, 201, 201, 200, 200, 185, 185, 185, 185, 176, 176, 111, 92, 92, 82, 32, 32, 1, 111, 111, 111, 111] 201
rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48])
total number of confs: 854
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051641 none CNC(=O)CCCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [39, 39, 21, 39, 15, 13, 10, 2, 2, 2, 1, 1, 1, 3, 5, 5, 5, 21, 42, 111, 111, 111, 111, 111, 1, 1, 39, 39, 39, 39, 21, 21, 15, 15, 15, 15, 10, 10, 2, 3, 3, 5, 21, 21, 111, 1, 1, 1, 1] 201
rigid atoms, others: [10, 11, 12, 45, 46, 47, 48, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 374
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051641 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051641
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051641/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051641
Building REAL300025051642
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051642'
/scratch/stefan/7786831/working/building/REAL300025051642 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051642

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051642/0 /scratch/stefan/7786831/working/building/REAL300025051642 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 516)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/516
`/scratch/stefan/7786831/working/3D/516' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025051642.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051642.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051642/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051642 none CC(C)(C)C1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 8, 8, 8, 8, 2, 2, 2, 1, 1, 1, 6, 13, 13, 13, 31, 39, 109, 109, 109, 109, 109, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 6, 6, 13, 31, 31, 109, 1, 1, 1, 1, 8, 8] 201
rigid atoms, others: [9, 10, 11, 46, 47, 48, 49, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51])
total number of confs: 260
number of broken/clashed sets: 201
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051642 none CC(C)(C)C1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 8, 8, 8, 8, 24, 44, 44, 44, 98, 114, 201, 201, 201, 201, 201, 8, 8, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 8, 24, 24, 44, 98, 98, 201, 8, 8, 8, 8, 1, 1] 201
rigid atoms, others: [1, 35, 4, 5, 6, 7, 50, 51, 25, 38, 37, 36] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 607
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051642 none CC(C)(C)C1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 109, 109, 109, 109, 81, 42, 42, 26, 42, 13, 1, 1, 1, 1, 1, 1, 1, 109, 109, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 109, 81, 81, 42, 26, 26, 1, 109, 109, 109, 109, 201, 201] 201
rigid atoms, others: [45, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51])
total number of confs: 698
number of broken/clashed sets: 201
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051642 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051642
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051642/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051642
Building REAL300025051643
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051643'
/scratch/stefan/7786831/working/building/REAL300025051643 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051643

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051643/0 /scratch/stefan/7786831/working/building/REAL300025051643 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 517)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/517
`/scratch/stefan/7786831/working/3D/517' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1C)

`REAL300025051643.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051643.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051643/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051643 none CC1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 6, 14, 14, 14, 36, 40, 122, 122, 122, 122, 122, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 6, 6, 14, 36, 36, 122, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7] 201
rigid atoms, others: [7, 8, 9, 42, 43, 44, 45, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 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, 41, 46, 47, 48, 49, 50, 51])
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: REAL300025051643 none CC1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 7, 7, 24, 49, 49, 49, 114, 125, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 24, 24, 49, 114, 114, 201, 7, 7, 7, 7, 1, 1, 1, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 46, 47, 48, 23, 24, 25, 5, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 49, 50, 51])
total number of confs: 644
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051643 none CC1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 122, 122, 122, 88, 44, 44, 28, 44, 13, 1, 1, 1, 1, 1, 1, 1, 122, 122, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 122, 88, 88, 44, 28, 28, 1, 122, 122, 122, 122, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [41, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 725
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051643 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051643
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051643/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051643
Building REAL300025051644
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051644'
/scratch/stefan/7786831/working/building/REAL300025051644 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051644

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051644/0 /scratch/stefan/7786831/working/building/REAL300025051644 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 518)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/518
`/scratch/stefan/7786831/working/3D/518' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1CCCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051644.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051644.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051644/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051644 none COC1CCCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 6, 22, 22, 22, 68, 95, 183, 183, 183, 183, 183, 1, 1, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 22, 68, 68, 183, 1, 1, 1, 1] 201
rigid atoms, others: [10, 11, 12, 46, 47, 48, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 447
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051644 none COC1CCCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 10, 31, 31, 31, 87, 115, 201, 201, 201, 201, 201, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 10, 10, 31, 87, 87, 201, 3, 3, 3, 3] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 34, 37, 35, 36, 33, 38, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 526
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051644 none COC1CCCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 183, 183, 183, 183, 144, 77, 77, 31, 77, 13, 1, 1, 1, 1, 1, 1, 1, 183, 183, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 183, 144, 144, 77, 31, 31, 1, 183, 183, 183, 183] 201
rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49])
total number of confs: 768
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051644 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051644
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051644/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051644
Building REAL300025051645
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051645'
/scratch/stefan/7786831/working/building/REAL300025051645 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051645

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051645/0 /scratch/stefan/7786831/working/building/REAL300025051645 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 519)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/519
`/scratch/stefan/7786831/working/3D/519' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)[NH+]1C(C)CCC1C)

`REAL300025051645.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051645.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051645/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051645 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)[NH+]1C(C)CCC1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 82, 67, 67, 36, 67, 13, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 82, 82, 67, 36, 36, 1, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87] 87
rigid atoms, others: [38, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 318
number of broken/clashed sets: 87
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051645 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)[NH+]1C(C)CCC1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [5, 2, 2, 2, 1, 1, 1, 5, 12, 12, 12, 39, 51, 87, 87, 87, 87, 87, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 5, 5, 12, 39, 39, 87, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 87
rigid atoms, others: [4, 5, 6, 39, 40, 41, 42, 18, 19] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 248
number of broken/clashed sets: 87
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051645 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)[NH+]1C(C)CCC1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 5, 5, 5, 5, 10, 18, 18, 18, 47, 55, 87, 87, 87, 87, 87, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 10, 10, 18, 47, 47, 87, 5, 5, 5, 5, 1, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2] 87
rigid atoms, others: [1, 43, 47, 48, 49, 50, 51, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 52, 53, 54])
total number of confs: 279
number of broken/clashed sets: 87
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051645 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051645
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051645/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051645
Building REAL300025051646
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051646'
/scratch/stefan/7786831/working/building/REAL300025051646 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051646

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051646/0 /scratch/stefan/7786831/working/building/REAL300025051646 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 520)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/520
`/scratch/stefan/7786831/working/3D/520' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCCOCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051646.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051646.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051646/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051646 none C=CCCOCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 153, 115, 66, 62, 62, 62, 62, 53, 25, 25, 23, 25, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 201, 201, 201, 201, 201, 153, 153, 66, 66, 62, 53, 53, 25, 23, 23, 1, 62, 62, 62, 62] 201
rigid atoms, others: [39, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 807
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051646 none C=CCCOCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [72, 46, 22, 9, 3, 2, 2, 2, 1, 1, 1, 4, 14, 14, 14, 24, 24, 62, 62, 62, 62, 62, 1, 1, 72, 72, 72, 46, 46, 22, 22, 3, 3, 2, 4, 4, 14, 24, 24, 62, 1, 1, 1, 1] 201
rigid atoms, others: [8, 9, 10, 43, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
total number of confs: 433
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051646 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051646
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051646/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051646
Building REAL300025051647
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051647'
/scratch/stefan/7786831/working/building/REAL300025051647 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051647

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051647/0 /scratch/stefan/7786831/working/building/REAL300025051647 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 521)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/521
`/scratch/stefan/7786831/working/3D/521' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCOC(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051647.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051647.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051647/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051647 none C=CCOC(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 173, 167, 115, 167, 115, 115, 115, 96, 60, 60, 26, 60, 13, 1, 1, 1, 1, 1, 1, 1, 115, 115, 201, 201, 201, 201, 201, 167, 167, 167, 167, 115, 96, 96, 60, 26, 26, 1, 115, 115, 115, 115] 201
rigid atoms, others: [39, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 911
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051647 none C=CCOC(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 16, 6, 4, 2, 4, 2, 2, 1, 1, 1, 4, 6, 6, 6, 22, 35, 115, 115, 115, 115, 115, 1, 1, 24, 24, 24, 16, 16, 4, 4, 4, 4, 2, 4, 4, 6, 22, 22, 115, 1, 1, 1, 1] 201
rigid atoms, others: [8, 9, 10, 43, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
total number of confs: 301
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051647 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051647
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051647/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051647
Building REAL300025051648
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051648'
/scratch/stefan/7786831/working/building/REAL300025051648 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051648

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051648/0 /scratch/stefan/7786831/working/building/REAL300025051648 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 522)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/522
`/scratch/stefan/7786831/working/3D/522' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CCOC(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051648.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051648.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051648/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051648 none CC(C)CCOC(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 149, 133, 114, 103, 114, 103, 103, 103, 90, 70, 70, 47, 70, 13, 1, 1, 1, 1, 1, 1, 1, 103, 103, 201, 201, 201, 201, 201, 201, 201, 201, 201, 149, 149, 114, 114, 114, 114, 103, 90, 90, 70, 47, 47, 1, 103, 103, 103, 103] 201
rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51])
total number of confs: 908
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051648 none CC(C)CCOC(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 15, 9, 4, 3, 2, 3, 2, 2, 1, 1, 1, 4, 13, 13, 13, 30, 46, 103, 103, 103, 103, 103, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 9, 3, 3, 3, 3, 2, 4, 4, 13, 30, 30, 103, 1, 1, 1, 1] 201
rigid atoms, others: [10, 11, 12, 48, 49, 50, 51, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 303
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051648 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051648
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051648/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051648
Building REAL300025051649
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051649'
/scratch/stefan/7786831/working/building/REAL300025051649 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051649

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051649/0 /scratch/stefan/7786831/working/building/REAL300025051649 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 523)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/523
`/scratch/stefan/7786831/working/3D/523' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OCC1CCCO1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051649.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051649.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051649/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051649 none CC(OCC1CCCO1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 2, 4, 6, 10, 13, 13, 13, 13, 2, 2, 1, 1, 1, 6, 19, 19, 19, 53, 82, 162, 162, 162, 162, 162, 1, 1, 4, 4, 4, 4, 10, 10, 13, 13, 13, 13, 13, 13, 13, 2, 6, 6, 19, 53, 53, 162, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 47, 48, 49, 50, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025051649 none CC(OCC1CCCO1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 8, 3, 1, 1, 1, 1, 1, 1, 10, 13, 13, 13, 13, 22, 46, 46, 46, 83, 118, 201, 201, 201, 201, 201, 13, 13, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 1, 1, 1, 13, 22, 22, 46, 83, 83, 201, 13, 13, 13, 13] 201
rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 39, 35, 36, 38, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 518
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051649 none CC(OCC1CCCO1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [169, 162, 169, 177, 191, 201, 201, 201, 201, 162, 162, 162, 141, 101, 101, 49, 101, 13, 1, 1, 1, 1, 1, 1, 1, 162, 162, 169, 169, 169, 169, 191, 191, 201, 201, 201, 201, 201, 201, 201, 162, 141, 141, 101, 49, 49, 1, 162, 162, 162, 162] 201
rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50])
total number of confs: 780
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051649 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051649
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051649/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051649
Building REAL300025051650
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051650'
/scratch/stefan/7786831/working/building/REAL300025051650 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051650

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051650/0 /scratch/stefan/7786831/working/building/REAL300025051650 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 524)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/524
`/scratch/stefan/7786831/working/3D/524' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=NC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1)

`REAL300025051650.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051650.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051650/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051650 none CCC1=NC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 6, 11, 11, 11, 40, 63, 136, 136, 136, 136, 136, 1, 1, 4, 9, 9, 9, 9, 9, 4, 2, 6, 6, 11, 40, 40, 136, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 8, 9, 10, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
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: REAL300025051650 none CCC1=NC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 9, 14, 14, 14, 43, 66, 137, 137, 137, 137, 137, 4, 4, 1, 6, 6, 6, 5, 5, 1, 4, 9, 9, 14, 43, 43, 137, 4, 4, 4, 4] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 24, 30] set([0, 7, 8, 9, 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, 40, 41])
total number of confs: 327
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051650 none CCC1=NC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 137, 137, 137, 137, 136, 136, 136, 136, 120, 66, 66, 28, 66, 13, 1, 1, 1, 1, 1, 1, 1, 136, 136, 137, 201, 201, 201, 201, 201, 137, 136, 120, 120, 66, 28, 28, 1, 136, 136, 136, 136] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41])
total number of confs: 909
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051650 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051650
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051650/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051650
Building REAL300025051651
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051651'
/scratch/stefan/7786831/working/building/REAL300025051651 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051651

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051651/0 /scratch/stefan/7786831/working/building/REAL300025051651 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 525)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/525
`/scratch/stefan/7786831/working/3D/525' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=C2CCC3)CC1)

`REAL300025051651.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051651.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051651/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051651 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=C2CCC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 18, 59, 69, 137, 137, 137, 137, 137, 5, 1, 1, 1, 3, 3, 3, 17, 17, 8, 17, 17, 17, 17, 17, 1, 1, 59, 59, 137, 18, 5, 5, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
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: REAL300025051651 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=C2CCC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [59, 30, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 117, 137, 137, 137, 137, 201, 201, 201, 201, 201, 201, 201, 201, 137, 137, 30, 30, 1, 59, 117, 117, 137, 201, 201, 201, 201, 201, 201, 201, 201, 201, 137, 137, 137, 137] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46])
total number of confs: 630
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051651 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=C2CCC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [65, 65, 65, 152, 164, 201, 201, 201, 201, 201, 24, 17, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 152, 152, 201, 65, 24, 24, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46])
total number of confs: 693
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051651 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051651
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051651/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051651
Building REAL300025051652
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051652'
/scratch/stefan/7786831/working/building/REAL300025051652 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051652

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051652/0 /scratch/stefan/7786831/working/building/REAL300025051652 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 526)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/526
`/scratch/stefan/7786831/working/3D/526' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCOCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051652.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051652.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051652/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051652 none COCCOCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 170, 124, 71, 71, 60, 60, 60, 60, 37, 19, 19, 9, 19, 8, 1, 1, 1, 1, 1, 1, 1, 60, 60, 201, 201, 201, 201, 201, 170, 170, 71, 71, 71, 71, 60, 37, 37, 19, 9, 9, 1, 60, 60, 60, 60] 201
rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46])
total number of confs: 778
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051652 none COCCOCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [65, 47, 31, 11, 4, 4, 2, 2, 2, 1, 1, 1, 6, 13, 13, 13, 29, 31, 60, 60, 60, 60, 60, 1, 1, 65, 65, 65, 47, 47, 31, 31, 4, 4, 4, 4, 2, 6, 6, 13, 29, 29, 60, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 46, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 395
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051652 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051652
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051652/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051652
Building REAL300025051653
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051653'
/scratch/stefan/7786831/working/building/REAL300025051653 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051653

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051653/0 /scratch/stefan/7786831/working/building/REAL300025051653 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 527)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/527
`/scratch/stefan/7786831/working/3D/527' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCCCC1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051653.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051653.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051653/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051653 none CC1CCCCC1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 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.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 1, 1, 1, 6, 9, 9, 9, 32, 45, 119, 119, 119, 119, 119, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 6, 6, 9, 32, 32, 119, 1, 1, 1, 1] 201
rigid atoms, others: [10, 11, 12, 48, 49, 50, 51, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
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: REAL300025051653 none CC1CCCCC1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 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.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 10, 10, 10, 10, 28, 37, 37, 37, 88, 114, 201, 201, 201, 201, 201, 10, 10, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 28, 28, 37, 88, 88, 201, 10, 10, 10, 10] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 34, 37, 35, 36, 38, 5, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 566
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051653 none CC1CCCCC1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 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.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 119, 119, 119, 119, 98, 61, 61, 28, 61, 13, 1, 1, 1, 1, 1, 1, 1, 119, 119, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 119, 98, 98, 61, 28, 28, 1, 119, 119, 119, 119] 201
rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51])
total number of confs: 876
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051653 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051653
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051653/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051653
Building REAL300025051654
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051654'
/scratch/stefan/7786831/working/building/REAL300025051654 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051654

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051654/0 /scratch/stefan/7786831/working/building/REAL300025051654 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 528)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/528
`/scratch/stefan/7786831/working/3D/528' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CC=CC=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051654.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051654.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051654/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051654 none O=C(CCC1=CC=CC=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 9, 16, 27, 27, 27, 27, 27, 1, 1, 1, 4, 12, 12, 12, 40, 66, 152, 152, 152, 152, 152, 1, 1, 9, 9, 16, 16, 27, 27, 27, 27, 2, 4, 4, 12, 40, 40, 152, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 10, 11, 12, 44, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 410
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051654 none O=C(CCC1=CC=CC=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 12, 6, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 35, 57, 57, 57, 106, 138, 201, 201, 201, 201, 201, 27, 27, 12, 12, 6, 6, 1, 1, 1, 1, 27, 35, 35, 57, 106, 106, 201, 27, 27, 27, 27] 201
rigid atoms, others: [32, 33, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 619
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051654 none O=C(CCC1=CC=CC=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [152, 152, 152, 195, 201, 201, 201, 201, 201, 201, 152, 124, 80, 80, 30, 80, 13, 1, 1, 1, 1, 1, 1, 1, 152, 152, 195, 195, 201, 201, 201, 201, 201, 201, 152, 124, 124, 80, 30, 30, 1, 152, 152, 152, 152] 201
rigid atoms, others: [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, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 818
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051654 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051654
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051654/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051654
Building REAL300025051655
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051655'
/scratch/stefan/7786831/working/building/REAL300025051655 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051655

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051655/0 /scratch/stefan/7786831/working/building/REAL300025051655 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 529)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/529
`/scratch/stefan/7786831/working/3D/529' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CSC=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051655.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051655.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051655/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051655 none O=C(CCC1=CSC=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 14, 1, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 10, 17, 26, 26, 26, 26, 1, 1, 1, 5, 9, 9, 9, 31, 51, 125, 125, 125, 125, 125, 1, 1, 10, 10, 17, 17, 26, 26, 2, 5, 5, 9, 31, 31, 125, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 352
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051655 none O=C(CCC1=CSC=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 14, 1, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 10, 4, 1, 1, 1, 1, 1, 1, 26, 26, 26, 41, 58, 58, 58, 115, 141, 201, 201, 201, 201, 201, 26, 26, 10, 10, 4, 4, 1, 1, 26, 41, 41, 58, 115, 115, 201, 26, 26, 26, 26] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 29, 30] set([0, 1, 2, 9, 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])
total number of confs: 652
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051655 none O=C(CCC1=CSC=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 14, 1, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [125, 125, 125, 193, 196, 201, 201, 201, 201, 125, 104, 56, 56, 27, 56, 13, 1, 1, 1, 1, 1, 1, 1, 125, 125, 193, 193, 196, 196, 201, 201, 125, 104, 104, 56, 27, 27, 1, 125, 125, 125, 125] 201
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41])
total number of confs: 857
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051655 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051655
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051655/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051655
Building REAL300025051656
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051656'
/scratch/stefan/7786831/working/building/REAL300025051656 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051656

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051656/0 /scratch/stefan/7786831/working/building/REAL300025051656 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 530)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/530
`/scratch/stefan/7786831/working/3D/530' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C(C)C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(C)=C1)

`REAL300025051656.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051656.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051656/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051656 none CC1=NN(C(C)C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 7, 2, 7, 2, 2, 1, 1, 1, 7, 23, 23, 23, 65, 76, 167, 167, 167, 167, 167, 1, 1, 10, 10, 10, 10, 10, 10, 7, 7, 7, 7, 2, 7, 7, 23, 65, 65, 167, 1, 1, 1, 1, 10, 10, 10, 10] 201
rigid atoms, others: [43, 8, 9, 10, 23, 44, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 45, 46, 47, 48])
total number of confs: 434
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051656 none CC1=NN(C(C)C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 25, 60, 60, 60, 126, 138, 201, 201, 201, 201, 201, 10, 10, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 10, 25, 25, 60, 126, 126, 201, 10, 10, 10, 10, 2, 2, 2, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 48, 24, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 671
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051656 none CC1=NN(C(C)C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 167, 201, 167, 167, 167, 117, 47, 47, 25, 47, 12, 1, 1, 1, 1, 1, 1, 1, 167, 167, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 167, 117, 117, 47, 25, 25, 1, 167, 167, 167, 167, 201, 201, 201, 201] 201
rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 808
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051656 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051656
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051656/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051656
Building REAL300025051657
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051657'
/scratch/stefan/7786831/working/building/REAL300025051657 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051657

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051657/0 /scratch/stefan/7786831/working/building/REAL300025051657 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 531)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/531
`/scratch/stefan/7786831/working/3D/531' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCC[NH+]1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051657.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051657.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051657/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051657 none O=C(CCCC[NH+]1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 6, 4, 6, 8, 14, 14, 14, 14, 14, 1, 1, 1, 5, 7, 7, 7, 24, 42, 94, 94, 94, 94, 94, 1, 1, 6, 6, 6, 6, 6, 6, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 2, 5, 5, 7, 24, 24, 94, 1, 1, 1, 1] 120
rigid atoms, others: [12, 13, 14, 51, 52, 53, 54, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 261
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: REAL300025051657 none O=C(CCCC[NH+]1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [14, 12, 7, 7, 5, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 18, 22, 22, 22, 54, 75, 120, 120, 120, 120, 120, 14, 14, 12, 12, 7, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 18, 18, 22, 54, 54, 120, 14, 14, 14, 14] 120
rigid atoms, others: [43, 36, 5, 6, 7, 8, 9, 10, 11, 40, 41, 39, 38, 42, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 347
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051657 none O=C(CCCC[NH+]1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [94, 94, 94, 116, 99, 116, 116, 120, 120, 120, 120, 120, 94, 85, 74, 74, 33, 74, 13, 1, 1, 1, 1, 1, 1, 1, 94, 94, 116, 116, 116, 116, 116, 116, 116, 116, 120, 120, 120, 120, 120, 120, 120, 120, 94, 85, 85, 74, 33, 33, 1, 94, 94, 94, 94] 120
rigid atoms, others: [50, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54])
total number of confs: 598
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051657 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051657
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051657/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051657
Building REAL300025051658
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051658'
/scratch/stefan/7786831/working/building/REAL300025051658 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051658

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051658/0 /scratch/stefan/7786831/working/building/REAL300025051658 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 532)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/532
`/scratch/stefan/7786831/working/3D/532' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=CC=C1)

`REAL300025051658.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051658.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051658/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051658 none CN(CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 194, 174, 174, 174, 174, 148, 81, 81, 40, 81, 13, 1, 1, 1, 1, 1, 1, 1, 174, 174, 201, 201, 201, 201, 201, 201, 201, 201, 201, 194, 194, 174, 148, 148, 81, 40, 40, 1, 174, 174, 174, 174, 201, 201, 201, 201, 201] 201
rigid atoms, others: [38, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 845
number of broken/clashed sets: 201
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051658 none CN(CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 6, 2, 2, 2, 1, 1, 1, 6, 22, 22, 22, 65, 80, 174, 174, 174, 174, 174, 1, 1, 7, 8, 8, 7, 8, 8, 7, 7, 7, 6, 6, 2, 6, 6, 22, 65, 65, 174, 1, 1, 1, 1, 8, 8, 8, 8, 8] 201
rigid atoms, others: [5, 6, 39, 40, 41, 42, 7, 19, 20] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47])
total number of confs: 430
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051658 none CN(CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 6, 8, 8, 8, 8, 17, 44, 44, 44, 99, 114, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 8, 17, 17, 44, 99, 99, 201, 8, 8, 8, 8, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 43, 44, 45, 46, 47, 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, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 551
number of broken/clashed sets: 201
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051658 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051658
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051658/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051658
Building REAL300025051659
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051659'
/scratch/stefan/7786831/working/building/REAL300025051659 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051659

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051659/0 /scratch/stefan/7786831/working/building/REAL300025051659 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 533)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/533
`/scratch/stefan/7786831/working/3D/533' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCC(NC(N)=O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051659.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051659.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051659/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051659 none CCCCC(NC(N)=O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 193, 148, 118, 148, 148, 148, 148, 118, 118, 118, 105, 65, 65, 32, 65, 13, 1, 1, 1, 1, 1, 1, 1, 118, 118, 201, 201, 201, 201, 201, 201, 201, 193, 193, 148, 148, 148, 148, 118, 105, 105, 65, 32, 32, 1, 118, 118, 118, 118] 201
rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50])
total number of confs: 934
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051659 none CCCCC(NC(N)=O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 16, 13, 5, 2, 5, 8, 8, 8, 2, 2, 1, 1, 1, 5, 9, 9, 9, 29, 44, 118, 118, 118, 118, 118, 1, 1, 22, 22, 22, 22, 22, 16, 16, 13, 13, 5, 8, 8, 8, 2, 5, 5, 9, 29, 29, 118, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 47, 48, 49, 50, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 354
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051659 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051659
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051659/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051659
Building REAL300025051660
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051660'
/scratch/stefan/7786831/working/building/REAL300025051660 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051660

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051660/0 /scratch/stefan/7786831/working/building/REAL300025051660 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 534)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/534
`/scratch/stefan/7786831/working/3D/534' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051660.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051660.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051660/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051660 none CN(C)C1=CC=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 4, 10, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 20, 20, 20, 64, 74, 187, 187, 187, 187, 187, 1, 1, 4, 10, 10, 10, 10, 10, 10, 4, 4, 2, 7, 7, 20, 64, 64, 187, 1, 1, 1, 1, 4] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46])
total number of confs: 453
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051660 none CN(C)C1=CC=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 12, 26, 26, 26, 76, 87, 201, 201, 201, 201, 201, 4, 4, 1, 5, 5, 5, 5, 5, 5, 1, 1, 4, 12, 12, 26, 76, 76, 201, 4, 4, 4, 4, 1] 201
rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 8, 7, 46, 26] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 503
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051660 none CN(C)C1=CC=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 187, 187, 187, 187, 108, 47, 47, 25, 47, 13, 1, 1, 1, 1, 1, 1, 1, 187, 187, 201, 201, 201, 201, 201, 201, 201, 201, 201, 187, 108, 108, 47, 25, 25, 1, 187, 187, 187, 187, 201] 201
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46])
total number of confs: 702
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051660 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051660
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051660/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051660
Building REAL300025051661
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051661'
/scratch/stefan/7786831/working/building/REAL300025051661 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051661

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051661/0 /scratch/stefan/7786831/working/building/REAL300025051661 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 535)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/535
`/scratch/stefan/7786831/working/3D/535' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCN1C=CN=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051661.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051661.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051661/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051661 none O=C(CCCN1C=CN=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 10, 14, 21, 36, 36, 36, 36, 1, 1, 1, 3, 5, 5, 5, 12, 16, 43, 43, 43, 43, 43, 1, 1, 10, 10, 18, 18, 19, 19, 36, 36, 36, 2, 3, 3, 5, 12, 12, 43, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
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: REAL300025051661 none O=C(CCCN1C=CN=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [36, 15, 10, 7, 1, 1, 1, 1, 1, 1, 36, 36, 36, 42, 50, 50, 50, 92, 116, 201, 201, 201, 201, 201, 36, 36, 15, 15, 10, 10, 7, 7, 1, 1, 1, 36, 42, 42, 50, 92, 92, 201, 36, 36, 36, 36] 201
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 631
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051661 none O=C(CCCN1C=CN=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [43, 43, 43, 97, 97, 117, 201, 201, 201, 201, 43, 36, 28, 28, 21, 28, 11, 1, 1, 1, 1, 1, 1, 1, 43, 43, 97, 97, 111, 111, 110, 112, 201, 201, 201, 43, 36, 36, 28, 21, 21, 1, 43, 43, 43, 43] 201
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 722
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051661 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051661
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051661/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051661
Building REAL300025051662
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051662'
/scratch/stefan/7786831/working/building/REAL300025051662 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051662

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051662/0 /scratch/stefan/7786831/working/building/REAL300025051662 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 536)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/536
`/scratch/stefan/7786831/working/3D/536' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC1=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CS1)

`REAL300025051662.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051662.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051662/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051662 none COCC1=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 12, 5, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 11, 4, 4, 4, 2, 2, 2, 1, 1, 1, 4, 7, 7, 7, 23, 39, 115, 115, 115, 115, 115, 1, 1, 4, 4, 21, 21, 21, 11, 11, 2, 4, 4, 7, 23, 23, 115, 1, 1, 1, 1, 4] 201
rigid atoms, others: [38, 39, 8, 9, 10, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 42])
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: REAL300025051662 none COCC1=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 12, 5, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 7, 1, 1, 1, 1, 1, 4, 4, 4, 4, 6, 9, 9, 9, 26, 42, 116, 116, 116, 116, 116, 4, 4, 1, 1, 16, 16, 16, 7, 7, 4, 6, 6, 9, 26, 26, 116, 4, 4, 4, 4, 1] 201
rigid atoms, others: [2, 3, 4, 5, 6, 42, 24, 25] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 276
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051662 none COCC1=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 12, 5, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 116, 116, 116, 115, 115, 115, 115, 87, 52, 52, 24, 52, 13, 1, 1, 1, 1, 1, 1, 1, 115, 115, 116, 116, 201, 201, 201, 201, 201, 115, 87, 87, 52, 24, 24, 1, 115, 115, 115, 115, 116] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 877
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051662 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051662
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051662/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051662
Building REAL300025051663
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051663'
/scratch/stefan/7786831/working/building/REAL300025051663 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051663

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051663/0 /scratch/stefan/7786831/working/building/REAL300025051663 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 537)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/537
`/scratch/stefan/7786831/working/3D/537' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=C1)

`REAL300025051663.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051663.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051663/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051663 none NC(=O)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 3, 3, 3, 2, 2, 2, 1, 1, 1, 7, 28, 28, 28, 78, 96, 172, 172, 172, 172, 172, 1, 1, 3, 3, 4, 4, 3, 3, 2, 7, 7, 28, 78, 78, 172, 1, 1, 1, 1, 3] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42])
total number of confs: 459
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051663 none NC(=O)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 3, 3, 3, 3, 11, 35, 35, 35, 88, 108, 176, 176, 176, 176, 176, 3, 3, 1, 1, 3, 3, 1, 1, 3, 11, 11, 35, 88, 88, 176, 3, 3, 3, 3, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 42, 25, 26, 29, 30] set([0, 2, 8, 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])
total number of confs: 494
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051663 none NC(=O)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 176, 201, 176, 176, 176, 172, 172, 172, 172, 119, 63, 63, 29, 63, 13, 1, 1, 1, 1, 1, 1, 1, 172, 172, 176, 176, 201, 201, 176, 176, 172, 119, 119, 63, 29, 29, 1, 172, 172, 172, 172, 176] 201
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 735
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051663 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051663
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051663/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051663
Building REAL300025051664
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051664'
/scratch/stefan/7786831/working/building/REAL300025051664 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051664

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051664/0 /scratch/stefan/7786831/working/building/REAL300025051664 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 538)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/538
`/scratch/stefan/7786831/working/3D/538' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCC(OCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1)

`REAL300025051664.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051664.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051664/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051664 none CC1CCC(OCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 22, 12, 5, 2, 2, 2, 1, 1, 1, 5, 11, 11, 11, 29, 36, 90, 90, 90, 90, 90, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 5, 5, 2, 5, 5, 11, 29, 29, 90, 1, 1, 1, 1, 22, 22, 22, 22] 201
rigid atoms, others: [9, 10, 11, 45, 46, 47, 48, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52])
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: REAL300025051664 none CC1CCC(OCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 4, 10, 22, 22, 22, 22, 43, 69, 69, 69, 113, 137, 201, 201, 201, 201, 201, 22, 22, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 10, 10, 22, 43, 43, 69, 113, 113, 201, 22, 22, 22, 22, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 51, 32, 34, 49, 50, 35, 52, 25, 26, 5, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 603
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051664 none CC1CCC(OCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 153, 121, 90, 90, 90, 90, 73, 64, 64, 38, 64, 13, 1, 1, 1, 1, 1, 1, 1, 90, 90, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 121, 121, 90, 73, 73, 64, 38, 38, 1, 90, 90, 90, 90, 201, 201, 201, 201] 201
rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 737
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051664 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051664
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051664/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051664
Building REAL300025051665
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051665'
/scratch/stefan/7786831/working/building/REAL300025051665 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051665

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051665/0 /scratch/stefan/7786831/working/building/REAL300025051665 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 539)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/539
`/scratch/stefan/7786831/working/3D/539' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CSC(C3CC3)=N2)CC1)

`REAL300025051665.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051665.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051665/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051665 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CSC(C3CC3)=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 14, 1, 5, 5, 5, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 17, 37, 39, 105, 105, 105, 105, 105, 4, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 56, 56, 13, 1, 1, 37, 37, 105, 17, 4, 4, 3, 13, 56, 56, 56, 56, 56, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 356
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051665 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CSC(C3CC3)=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 14, 1, 5, 5, 5, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [40, 29, 13, 1, 1, 1, 1, 1, 1, 1, 40, 40, 80, 105, 105, 105, 105, 150, 150, 150, 150, 201, 201, 150, 105, 105, 29, 29, 1, 40, 80, 80, 105, 150, 201, 201, 201, 201, 201, 105, 105, 105, 105] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 691
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051665 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CSC(C3CC3)=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 14, 1, 5, 5, 5, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [130, 130, 130, 172, 173, 201, 201, 201, 201, 201, 66, 56, 40, 40, 13, 40, 13, 13, 13, 1, 1, 1, 1, 13, 56, 56, 172, 172, 201, 130, 66, 66, 40, 13, 1, 1, 1, 1, 1, 56, 56, 56, 56] 201
rigid atoms, others: [34, 35, 36, 37, 38, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42])
total number of confs: 700
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051665 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CSC(C3CC3)=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 14, 1, 5, 5, 5, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [46, 46, 46, 83, 85, 150, 150, 150, 150, 150, 15, 13, 8, 7, 1, 7, 1, 1, 1, 1, 1, 13, 13, 1, 13, 13, 83, 83, 150, 46, 15, 15, 8, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13] 201
rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 460
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051665 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051665
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051665/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051665
Building REAL300025051666
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051666'
/scratch/stefan/7786831/working/building/REAL300025051666 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051666

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051666/0 /scratch/stefan/7786831/working/building/REAL300025051666 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 540)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/540
`/scratch/stefan/7786831/working/3D/540' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)OCCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051666.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051666.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051666/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051666 none CC(C)OCCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 176, 201, 150, 145, 144, 95, 95, 95, 95, 80, 63, 63, 30, 63, 13, 1, 1, 1, 1, 1, 1, 1, 95, 95, 201, 201, 201, 201, 201, 201, 201, 147, 148, 150, 150, 144, 144, 95, 80, 80, 63, 30, 30, 1, 95, 95, 95, 95] 201
rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48])
total number of confs: 843
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051666 none CC(C)OCCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [35, 22, 35, 13, 11, 9, 2, 2, 2, 1, 1, 1, 3, 5, 5, 5, 20, 34, 95, 95, 95, 95, 95, 1, 1, 35, 35, 35, 35, 35, 35, 35, 12, 12, 13, 13, 9, 9, 2, 3, 3, 5, 20, 20, 95, 1, 1, 1, 1] 201
rigid atoms, others: [9, 10, 11, 45, 46, 47, 48, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 329
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051666 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051666
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051666/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051666
Building REAL300025051667
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051667'
/scratch/stefan/7786831/working/building/REAL300025051667 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051667

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051667/0 /scratch/stefan/7786831/working/building/REAL300025051667 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 541)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/541
`/scratch/stefan/7786831/working/3D/541' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)CCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051667.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051667.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051667/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051667 none NC(=O)CCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 172, 156, 78, 78, 78, 78, 63, 53, 53, 28, 53, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 201, 201, 193, 198, 183, 183, 156, 156, 78, 63, 63, 53, 28, 28, 1, 78, 78, 78, 78] 201
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42])
total number of confs: 907
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051667 none NC(=O)CCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [34, 26, 34, 15, 10, 2, 2, 2, 1, 1, 1, 4, 6, 6, 6, 17, 27, 78, 78, 78, 78, 78, 1, 1, 34, 34, 23, 25, 18, 18, 10, 10, 2, 4, 4, 6, 17, 17, 78, 1, 1, 1, 1] 201
rigid atoms, others: [39, 8, 9, 10, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 309
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051667 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051667
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051667/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051667
Building REAL300025051668
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051668'
/scratch/stefan/7786831/working/building/REAL300025051668 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051668

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051668/0 /scratch/stefan/7786831/working/building/REAL300025051668 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 542)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/542
`/scratch/stefan/7786831/working/3D/542' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+]1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1)

`REAL300025051668.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051668.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051668/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051668 none C[NH+]1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
4  conformations in input
total number of sets (complete confs): 4
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 2, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 3, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 3] 4
rigid atoms, others: [43, 8, 9, 10, 23, 44, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 45, 46, 47, 48])
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: REAL300025051668 none C[NH+]1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
4  conformations in input
total number of sets (complete confs): 4
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 3, 3, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 4, 4, 3, 3, 3, 3, 1, 1, 1, 1] 4
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 45, 46, 47, 48, 24, 25, 33, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 19
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051668 none C[NH+]1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 3, 4, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 1, 4, 4, 4, 4, 4, 4, 4, 4] 4
rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 8
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051668 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051668
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051668/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051668
Building REAL300025051669
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051669'
/scratch/stefan/7786831/working/building/REAL300025051669 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051669

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051669/0 /scratch/stefan/7786831/working/building/REAL300025051669 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 543)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/543
`/scratch/stefan/7786831/working/3D/543' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1)

`REAL300025051669.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051669.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051669/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051669 none NC(=O)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 21, 21, 21, 78, 88, 171, 171, 171, 171, 171, 1, 1, 5, 5, 5, 5, 5, 5, 2, 4, 4, 21, 78, 78, 171, 1, 1, 1, 1, 5] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42])
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: REAL300025051669 none NC(=O)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 57, 57, 57, 145, 157, 201, 201, 201, 201, 201, 5, 5, 1, 1, 2, 2, 1, 1, 5, 13, 13, 57, 145, 145, 201, 5, 5, 5, 5, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 42, 25, 26, 29, 30] set([8, 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])
total number of confs: 649
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051669 none NC(=O)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 171, 171, 171, 171, 132, 73, 73, 30, 73, 13, 1, 1, 1, 1, 1, 1, 1, 171, 171, 201, 201, 201, 201, 201, 201, 171, 132, 132, 73, 30, 30, 1, 171, 171, 171, 171, 201] 201
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 696
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051669 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051669
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051669/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051669
Building REAL300025051670
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051670'
/scratch/stefan/7786831/working/building/REAL300025051670 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051670

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051670/0 /scratch/stefan/7786831/working/building/REAL300025051670 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 544)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/544
`/scratch/stefan/7786831/working/3D/544' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2COC3=CC=CC=C32)CC1)

`REAL300025051670.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051670.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051670/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051670 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2COC3=CC=CC=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 75, 89, 164, 164, 164, 164, 164, 6, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 75, 75, 164, 28, 6, 6, 3, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 42, 11, 12, 13, 44, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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])
total number of confs: 446
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051670 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2COC3=CC=CC=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 137, 164, 164, 164, 164, 201, 201, 201, 201, 201, 201, 201, 201, 164, 164, 32, 32, 1, 64, 137, 137, 164, 201, 201, 201, 201, 201, 201, 201, 164, 164, 164, 164] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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: 767
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051670 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2COC3=CC=CC=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 132, 142, 201, 201, 201, 201, 201, 20, 13, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 132, 132, 201, 65, 20, 20, 9, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44])
total number of confs: 624
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051670 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051670
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051670/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051670
Building REAL300025051671
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051671'
/scratch/stefan/7786831/working/building/REAL300025051671 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051671

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051671/0 /scratch/stefan/7786831/working/building/REAL300025051671 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 545)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/545
`/scratch/stefan/7786831/working/3D/545' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=COC3=CC=CC=C23)CC1)

`REAL300025051671.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051671.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051671/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051671 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=COC3=CC=CC=C23)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 19, 69, 84, 153, 153, 153, 153, 153, 5, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 69, 69, 153, 19, 5, 5, 3, 11, 11, 11, 11, 11, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 405
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051671 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=COC3=CC=CC=C23)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 35, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 124, 153, 153, 153, 153, 201, 201, 201, 201, 201, 201, 201, 201, 153, 153, 35, 35, 1, 69, 124, 124, 153, 201, 201, 201, 201, 201, 153, 153, 153, 153] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 661
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051671 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=COC3=CC=CC=C23)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 149, 161, 201, 201, 201, 201, 201, 19, 11, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 149, 149, 201, 64, 19, 19, 6, 1, 1, 1, 1, 1, 11, 11, 11, 11] 201
rigid atoms, others: [34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42])
total number of confs: 690
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051671 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051671
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051671/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051671
Building REAL300025051672
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051672'
/scratch/stefan/7786831/working/building/REAL300025051672 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051672

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051672/0 /scratch/stefan/7786831/working/building/REAL300025051672 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 546)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/546
`/scratch/stefan/7786831/working/3D/546' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC(=O)NCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051672.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051672.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051672/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051672 none CC(C)CC(=O)NCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 169, 169, 169, 169, 160, 87, 87, 87, 87, 67, 57, 57, 27, 57, 12, 1, 1, 1, 1, 1, 1, 1, 87, 87, 201, 201, 201, 201, 201, 201, 201, 201, 201, 169, 169, 169, 160, 160, 87, 67, 67, 57, 27, 27, 1, 87, 87, 87, 87] 201
rigid atoms, others: [47, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51])
total number of confs: 878
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051672 none CC(C)CC(=O)NCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [34, 33, 33, 12, 12, 12, 12, 9, 2, 2, 2, 1, 1, 1, 3, 4, 4, 4, 17, 32, 87, 87, 87, 87, 87, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 12, 12, 9, 9, 2, 3, 3, 4, 17, 17, 87, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 48, 49, 50, 51, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 309
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051672 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051672
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051672/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051672
Building REAL300025051673
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051673'
/scratch/stefan/7786831/working/building/REAL300025051673 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051673

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051673/0 /scratch/stefan/7786831/working/building/REAL300025051673 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 547)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/547
`/scratch/stefan/7786831/working/3D/547' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NNC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051673.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051673.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051673/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051673 none CC1=NNC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 21, 21, 21, 85, 99, 164, 164, 164, 164, 164, 1, 1, 5, 5, 5, 5, 5, 2, 4, 4, 21, 85, 85, 164, 1, 1, 1, 1] 182
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
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: REAL300025051673 none CC1=NNC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 11, 51, 51, 51, 126, 140, 182, 182, 182, 182, 182, 5, 5, 2, 2, 2, 1, 1, 5, 11, 11, 51, 126, 126, 182, 5, 5, 5, 5] 182
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 578
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051673 none CC1=NNC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [182, 182, 182, 182, 182, 164, 164, 164, 164, 140, 77, 77, 36, 77, 13, 1, 1, 1, 1, 1, 1, 1, 164, 164, 182, 182, 182, 182, 182, 164, 140, 140, 77, 36, 36, 1, 164, 164, 164, 164] 182
rigid atoms, others: [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, 33, 34, 36, 37, 38, 39])
total number of confs: 664
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051673 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051673
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051673/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051673
Building REAL300025051674
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051674'
/scratch/stefan/7786831/working/building/REAL300025051674 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051674

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051674/0 /scratch/stefan/7786831/working/building/REAL300025051674 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 548)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/548
`/scratch/stefan/7786831/working/3D/548' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051674.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051674.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051674/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051674 none CCCC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 10, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 6, 10, 10, 10, 37, 54, 121, 121, 121, 121, 121, 1, 1, 4, 12, 12, 12, 12, 12, 10, 10, 4, 2, 6, 6, 10, 37, 37, 121, 1, 1, 1, 1, 4] 201
rigid atoms, others: [43, 9, 10, 11, 44, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45])
total number of confs: 312
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051674 none CCCC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 4, 4, 4, 4, 10, 15, 15, 15, 45, 61, 125, 125, 125, 125, 125, 4, 4, 1, 8, 8, 8, 8, 8, 6, 6, 1, 4, 10, 10, 15, 45, 45, 125, 4, 4, 4, 4, 1] 201
rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 45, 25] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 333
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051674 none CCCC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 125, 125, 125, 125, 121, 121, 121, 121, 93, 57, 57, 27, 57, 12, 1, 1, 1, 1, 1, 1, 1, 121, 121, 125, 201, 201, 201, 201, 201, 201, 201, 125, 121, 93, 93, 57, 27, 27, 1, 121, 121, 121, 121, 125] 201
rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45])
total number of confs: 937
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051674 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051674
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051674/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051674
Building REAL300025051675
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051675'
/scratch/stefan/7786831/working/building/REAL300025051675 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051675

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051675/0 /scratch/stefan/7786831/working/building/REAL300025051675 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 549)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/549
`/scratch/stefan/7786831/working/3D/549' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=NNC=C32)CC1)

`REAL300025051675.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051675.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051675/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051675 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=NNC=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 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]
0  hydrogens 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, 52, 64, 144, 144, 144, 144, 144, 5, 1, 1, 1, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 52, 52, 144, 17, 5, 5, 3, 20, 20, 20, 20, 20, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
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: REAL300025051675 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=NNC=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [70, 31, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 130, 144, 144, 144, 144, 201, 201, 201, 201, 201, 201, 201, 201, 144, 144, 31, 31, 1, 70, 130, 130, 144, 201, 201, 201, 201, 201, 144, 144, 144, 144] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 654
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051675 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=NNC=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [74, 74, 74, 148, 157, 201, 201, 201, 201, 201, 29, 20, 11, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 148, 148, 201, 74, 29, 29, 11, 1, 1, 1, 1, 1, 20, 20, 20, 20] 201
rigid atoms, others: [34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42])
total number of confs: 694
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051675 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051675
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051675/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051675
Building REAL300025051676
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051676'
/scratch/stefan/7786831/working/building/REAL300025051676 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051676

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051676/0 /scratch/stefan/7786831/working/building/REAL300025051676 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 550)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/550
`/scratch/stefan/7786831/working/3D/550' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=CNN=C32)CC1)

`REAL300025051676.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051676.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051676/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051676 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=CNN=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 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]
0  hydrogens 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, 88, 97, 199, 199, 199, 199, 199, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 88, 88, 199, 27, 6, 6, 3, 7, 7, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 511
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051676 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=CNN=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 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]
0  hydrogens 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, 32, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 150, 199, 199, 199, 199, 201, 201, 201, 201, 201, 201, 201, 201, 199, 199, 32, 32, 1, 62, 150, 150, 199, 201, 201, 201, 201, 201, 199, 199, 199, 199] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 761
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051676 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=CNN=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [51, 51, 51, 131, 139, 201, 201, 201, 201, 201, 14, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 131, 131, 201, 51, 14, 14, 4, 1, 1, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42])
total number of confs: 633
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051676 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051676
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051676/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051676
Building REAL300025051677
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051677'
/scratch/stefan/7786831/working/building/REAL300025051677 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051677

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051677/0 /scratch/stefan/7786831/working/building/REAL300025051677 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 551)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/551
`/scratch/stefan/7786831/working/3D/551' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3N=CC=CN3N=C2)CC1)

`REAL300025051677.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051677.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051677/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051677 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3N=CC=CN3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 30, 102, 115, 198, 198, 198, 198, 198, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 102, 102, 198, 30, 6, 6, 3, 7, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 541
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051677 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3N=CC=CN3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [77, 34, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 154, 198, 198, 198, 198, 201, 201, 201, 201, 201, 201, 201, 201, 198, 198, 34, 34, 1, 77, 154, 154, 198, 201, 201, 201, 201, 198, 198, 198, 198] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 735
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051677 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3N=CC=CN3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 48, 134, 144, 201, 201, 201, 201, 201, 14, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 134, 134, 201, 48, 14, 14, 4, 1, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 643
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051677 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051677
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051677/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051677
Building REAL300025051678
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051678'
/scratch/stefan/7786831/working/building/REAL300025051678 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051678

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051678/0 /scratch/stefan/7786831/working/building/REAL300025051678 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 552)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/552
`/scratch/stefan/7786831/working/3D/552' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1)

`REAL300025051678.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051678.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051678/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051678 none C#CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
194  conformations in input
total number of sets (complete confs): 194
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 3, 3, 2, 2, 2, 1, 1, 1, 4, 22, 22, 22, 104, 132, 194, 194, 194, 194, 194, 1, 1, 3, 3, 2, 3, 3, 2, 4, 4, 22, 104, 104, 194, 1, 1, 1, 1, 3, 3] 194
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41])
total number of confs: 534
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051678 none C#CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
151  conformations in input
total number of sets (complete confs): 151
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 8, 37, 37, 37, 96, 116, 151, 151, 151, 151, 151, 4, 4, 1, 1, 1, 1, 1, 4, 8, 8, 37, 96, 96, 151, 4, 4, 4, 4, 1, 1] 151
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 40, 41, 24, 25, 26, 27, 28] set([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])
total number of confs: 455
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051678 none C#CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 194, 194, 194, 157, 87, 87, 32, 87, 13, 1, 1, 1, 1, 1, 1, 1, 194, 194, 194, 194, 194, 194, 194, 194, 157, 157, 87, 32, 32, 1, 194, 194, 194, 194, 194, 194] 194
rigid atoms, others: [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, 33, 34, 36, 37, 38, 39, 40, 41])
total number of confs: 711
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051678 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051678
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051678/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051678
Building REAL300025051679
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051679'
/scratch/stefan/7786831/working/building/REAL300025051679 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051679

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051679/0 /scratch/stefan/7786831/working/building/REAL300025051679 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 553)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/553
`/scratch/stefan/7786831/working/3D/553' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)NN=N1)

`REAL300025051679.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051679.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051679/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051679 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)NN=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 2, 2, 2, 1, 1, 1, 4, 15, 15, 15, 28, 31, 47, 47, 47, 47, 47, 1, 1, 8, 8, 8, 8, 8, 8, 2, 4, 4, 15, 28, 28, 47, 1, 1, 1, 1, 8] 58
rigid atoms, others: [34, 35, 36, 5, 6, 7, 19, 20, 37] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38])
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: REAL300025051679 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)NN=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
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, 8, 8, 8, 8, 15, 30, 30, 30, 45, 46, 58, 58, 58, 58, 58, 8, 8, 1, 1, 1, 2, 2, 2, 8, 15, 15, 30, 45, 45, 58, 8, 8, 8, 8, 1] 58
rigid atoms, others: [0, 1, 2, 3, 38, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 206
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051679 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)NN=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [58, 58, 47, 47, 47, 47, 45, 33, 33, 20, 33, 12, 1, 1, 1, 1, 1, 1, 1, 47, 47, 58, 58, 58, 58, 58, 58, 47, 45, 45, 33, 20, 20, 1, 47, 47, 47, 47, 58] 58
rigid atoms, others: [33, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 199
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051679 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051679/1 /scratch/stefan/7786831/working/building/REAL300025051679 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 554)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/554
`/scratch/stefan/7786831/working/3D/554' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NNN=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051679.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051679.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051679/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051679 none CC1=NNN=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 8, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 5, 25, 25, 25, 108, 134, 199, 199, 199, 199, 199, 1, 1, 4, 4, 4, 4, 2, 5, 5, 25, 108, 108, 199, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
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: REAL300025051679 none CC1=NNN=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 8, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 41, 41, 41, 126, 147, 201, 201, 201, 201, 201, 4, 4, 2, 2, 2, 1, 4, 11, 11, 41, 126, 126, 201, 4, 4, 4, 4] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 604
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051679 none CC1=NNN=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 8, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 199, 199, 199, 199, 171, 74, 74, 31, 74, 13, 1, 1, 1, 1, 1, 1, 1, 199, 199, 201, 201, 201, 201, 199, 171, 171, 74, 31, 31, 1, 199, 199, 199, 199] 201
rigid atoms, others: [34, 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, 35, 36, 37, 38])
total number of confs: 753
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051679 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051679
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051679/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051679/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051679
Building REAL300025051680
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051680'
/scratch/stefan/7786831/working/building/REAL300025051680 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051680

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051680/0 /scratch/stefan/7786831/working/building/REAL300025051680 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 555)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/555
`/scratch/stefan/7786831/working/3D/555' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051680.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051680.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051680/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051680 none COC1=CC=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 27, 27, 27, 74, 82, 193, 193, 193, 193, 193, 1, 1, 4, 6, 6, 6, 4, 4, 2, 7, 7, 27, 74, 74, 193, 1, 1, 1, 1, 4] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42])
total number of confs: 469
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051680 none COC1=CC=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 13, 38, 38, 38, 91, 100, 201, 201, 201, 201, 201, 4, 4, 1, 3, 3, 3, 1, 1, 4, 13, 13, 38, 91, 91, 201, 4, 4, 4, 4, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 42, 25, 29, 30] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 526
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051680 none COC1=CC=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 193, 193, 193, 193, 117, 48, 48, 26, 48, 12, 1, 1, 1, 1, 1, 1, 1, 193, 193, 201, 201, 201, 201, 201, 201, 193, 117, 117, 48, 26, 26, 1, 193, 193, 193, 193, 201] 201
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 717
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051680 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051680
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051680/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051680
Building REAL300025051681
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051681'
/scratch/stefan/7786831/working/building/REAL300025051681 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051681

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051681/0 /scratch/stefan/7786831/working/building/REAL300025051681 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 556)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/556
`/scratch/stefan/7786831/working/3D/556' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CSC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051681.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051681.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051681/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051681 none COC1=CSC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 14, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 27, 27, 27, 75, 84, 196, 196, 196, 196, 196, 1, 1, 4, 5, 5, 5, 4, 2, 7, 7, 27, 75, 75, 196, 1, 1, 1, 1, 4] 201
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40])
total number of confs: 481
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051681 none COC1=CSC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 14, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 13, 38, 38, 38, 90, 99, 201, 201, 201, 201, 201, 4, 4, 1, 3, 3, 3, 1, 4, 13, 13, 38, 90, 90, 201, 4, 4, 4, 4, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 24, 28] set([0, 7, 8, 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])
total number of confs: 539
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051681 none COC1=CSC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 14, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 196, 196, 196, 196, 122, 47, 47, 28, 47, 13, 1, 1, 1, 1, 1, 1, 1, 196, 196, 201, 201, 201, 201, 201, 196, 122, 122, 47, 28, 28, 1, 196, 196, 196, 196, 201] 201
rigid atoms, others: [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, 33, 34, 36, 37, 38, 39, 40])
total number of confs: 747
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051681 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051681
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051681/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051681
Building REAL300025051682
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051682'
/scratch/stefan/7786831/working/building/REAL300025051682 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051682

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051682/0 /scratch/stefan/7786831/working/building/REAL300025051682 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 557)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/557
`/scratch/stefan/7786831/working/3D/557' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(=O)CCC1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051682.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051682.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051682/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051682 none CN1C(=O)CCC1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 8, 2, 2, 2, 1, 1, 1, 7, 13, 13, 13, 36, 49, 138, 138, 138, 138, 138, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 8, 8, 2, 7, 7, 13, 36, 36, 138, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 331
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051682 none CN1C(=O)CCC1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 12, 12, 12, 12, 35, 46, 46, 46, 103, 127, 201, 201, 201, 201, 201, 12, 12, 2, 2, 2, 1, 1, 1, 1, 1, 3, 3, 12, 35, 35, 46, 103, 103, 201, 12, 12, 12, 12] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 33, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 614
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051682 none CN1C(=O)CCC1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 138, 138, 138, 138, 108, 58, 58, 27, 58, 13, 1, 1, 1, 1, 1, 1, 1, 138, 138, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 138, 108, 108, 58, 27, 27, 1, 138, 138, 138, 138] 201
rigid atoms, others: [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, 40, 41, 43, 44, 45, 46])
total number of confs: 882
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051682 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051682
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051682/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051682
Building REAL300025051683
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051683'
/scratch/stefan/7786831/working/building/REAL300025051683 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051683

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051683/0 /scratch/stefan/7786831/working/building/REAL300025051683 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 558)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/558
`/scratch/stefan/7786831/working/3D/558' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CC=CC=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051683.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051683.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051683/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051683 none O=C(CCC1=CC=CC=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 9, 16, 27, 27, 27, 27, 27, 1, 1, 1, 4, 12, 12, 12, 40, 66, 152, 152, 152, 152, 152, 1, 1, 9, 9, 16, 16, 27, 27, 27, 27, 2, 4, 4, 12, 40, 40, 152, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 10, 11, 12, 44, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 410
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051683 none O=C(CCC1=CC=CC=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 12, 6, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 35, 57, 57, 57, 106, 138, 201, 201, 201, 201, 201, 27, 27, 12, 12, 6, 6, 1, 1, 1, 1, 27, 35, 35, 57, 106, 106, 201, 27, 27, 27, 27] 201
rigid atoms, others: [32, 33, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 619
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051683 none O=C(CCC1=CC=CC=N1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [152, 152, 152, 195, 201, 201, 201, 201, 201, 201, 152, 124, 80, 80, 30, 80, 13, 1, 1, 1, 1, 1, 1, 1, 152, 152, 195, 195, 201, 201, 201, 201, 201, 201, 152, 124, 124, 80, 30, 30, 1, 152, 152, 152, 152] 201
rigid atoms, others: [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, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 818
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051683 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051683
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051683/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051683
Building REAL300025051684
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051684'
/scratch/stefan/7786831/working/building/REAL300025051684 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051684

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051684/0 /scratch/stefan/7786831/working/building/REAL300025051684 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 559)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/559
`/scratch/stefan/7786831/working/3D/559' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=NN=NN3C=C2)CC1)

`REAL300025051684.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051684.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051684/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051684 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=NN=NN3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 8, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 67, 78, 127, 127, 127, 127, 127, 6, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 67, 67, 127, 24, 6, 6, 3, 9, 9, 9, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 361
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051684 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=NN=NN3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 8, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [65, 30, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 100, 127, 127, 127, 127, 201, 201, 201, 201, 201, 201, 201, 201, 127, 127, 30, 30, 1, 65, 100, 100, 127, 201, 201, 201, 127, 127, 127, 127] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 576
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051684 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=NN=NN3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 8, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [70, 70, 70, 153, 170, 201, 201, 201, 201, 201, 18, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 153, 153, 201, 70, 18, 18, 5, 1, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [34, 35, 36, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40])
total number of confs: 687
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051684 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051684
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051684/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051684
Building REAL300025051685
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051685'
/scratch/stefan/7786831/working/building/REAL300025051685 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051685

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051685/0 /scratch/stefan/7786831/working/building/REAL300025051685 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 560)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/560
`/scratch/stefan/7786831/working/3D/560' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=NN(C)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051685.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051685.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051685/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051685 none COC1=NN(C)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 29, 29, 29, 81, 91, 191, 191, 191, 191, 191, 1, 1, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 29, 81, 81, 191, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 10, 11, 12, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 482
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051685 none COC1=NN(C)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 16, 49, 49, 49, 113, 124, 201, 201, 201, 201, 201, 4, 4, 2, 2, 2, 2, 2, 2, 1, 4, 16, 16, 49, 113, 113, 201, 4, 4, 4, 4] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 610
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051685 none COC1=NN(C)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 191, 191, 191, 191, 119, 46, 46, 28, 46, 13, 1, 1, 1, 1, 1, 1, 1, 191, 191, 201, 201, 201, 201, 201, 201, 201, 191, 119, 119, 46, 28, 28, 1, 191, 191, 191, 191] 201
rigid atoms, others: [39, 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, 40, 41, 42, 43])
total number of confs: 724
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051685 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051685
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051685/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051685
Building REAL300025051686
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051686'
/scratch/stefan/7786831/working/building/REAL300025051686 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051686

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051686/0 /scratch/stefan/7786831/working/building/REAL300025051686 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 561)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/561
`/scratch/stefan/7786831/working/3D/561' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(OC)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051686.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051686.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051686/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051686 none CCCC(OC)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 196, 175, 128, 175, 177, 128, 128, 128, 103, 64, 64, 29, 64, 13, 1, 1, 1, 1, 1, 1, 1, 128, 128, 201, 201, 201, 201, 201, 201, 201, 175, 177, 177, 177, 128, 103, 103, 64, 29, 29, 1, 128, 128, 128, 128] 201
rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 954
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051686 none CCCC(OC)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 13, 5, 2, 5, 7, 2, 2, 1, 1, 1, 4, 9, 9, 9, 28, 46, 128, 128, 128, 128, 128, 1, 1, 15, 15, 15, 15, 15, 14, 14, 5, 7, 7, 7, 2, 4, 4, 9, 28, 28, 128, 1, 1, 1, 1] 201
rigid atoms, others: [8, 9, 10, 43, 44, 45, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
total number of confs: 314
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051686 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051686
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051686/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051686
Building REAL300025051687
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051687'
/scratch/stefan/7786831/working/building/REAL300025051687 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051687

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051687/0 /scratch/stefan/7786831/working/building/REAL300025051687 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 562)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/562
`/scratch/stefan/7786831/working/3D/562' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C(C)CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1)

`REAL300025051687.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051687.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051687/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051687 none CC1=NN(C(C)CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 17, 8, 5, 8, 2, 2, 2, 1, 1, 1, 3, 7, 7, 7, 30, 58, 142, 142, 142, 142, 142, 1, 1, 17, 17, 17, 17, 17, 8, 8, 8, 8, 5, 5, 2, 3, 3, 7, 30, 30, 142, 1, 1, 1, 1, 17, 17] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 46, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48])
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: REAL300025051687 none CC1=NN(C(C)CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 7, 17, 17, 17, 17, 27, 44, 44, 44, 109, 147, 201, 201, 201, 201, 201, 17, 17, 1, 1, 2, 2, 2, 5, 5, 5, 5, 7, 7, 17, 27, 27, 44, 109, 109, 201, 17, 17, 17, 17, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 47, 48, 25, 26] set([5, 6, 7, 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, 42, 43, 44, 45, 46])
total number of confs: 635
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051687 none CC1=NN(C(C)CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 200, 189, 200, 142, 142, 142, 142, 120, 96, 96, 54, 96, 13, 1, 1, 1, 1, 1, 1, 1, 142, 142, 201, 201, 201, 201, 201, 200, 200, 200, 200, 189, 189, 142, 120, 120, 96, 54, 54, 1, 142, 142, 142, 142, 201, 201] 201
rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48])
total number of confs: 875
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051687 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051687
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051687/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051687
Building REAL300025051688
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051688'
/scratch/stefan/7786831/working/building/REAL300025051688 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051688

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051688/0 /scratch/stefan/7786831/working/building/REAL300025051688 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 563)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/563
`/scratch/stefan/7786831/working/3D/563' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2CCNC(=O)C2)CC1)

`REAL300025051688.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051688.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051688/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051688 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2CCNC(=O)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 69, 86, 176, 176, 176, 176, 176, 6, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 1, 1, 69, 69, 176, 24, 6, 6, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 459
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: REAL300025051688 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2CCNC(=O)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [88, 34, 13, 1, 1, 1, 1, 1, 1, 1, 88, 88, 146, 176, 176, 176, 176, 201, 201, 201, 201, 201, 201, 201, 176, 176, 34, 34, 1, 88, 146, 146, 176, 201, 201, 201, 201, 201, 201, 201, 201, 201, 176, 176, 176, 176] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 789
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051688 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2CCNC(=O)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 141, 158, 201, 201, 201, 201, 201, 21, 13, 8, 8, 4, 8, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 141, 141, 201, 65, 21, 21, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13] 201
rigid atoms, others: [35, 36, 37, 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, 42, 43, 44, 45])
total number of confs: 667
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051688 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051688
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051688/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051688
Building REAL300025051689
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051689'
/scratch/stefan/7786831/working/building/REAL300025051689 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051689

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051689/0 /scratch/stefan/7786831/working/building/REAL300025051689 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 564)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/564
`/scratch/stefan/7786831/working/3D/564' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCCCC(CC)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051689.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051689.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051689/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051689 none CCCCCCC(CC)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 175, 108, 175, 174, 108, 108, 108, 90, 65, 65, 49, 65, 13, 1, 1, 1, 1, 1, 1, 1, 108, 108, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 175, 175, 175, 175, 175, 175, 108, 90, 90, 65, 49, 49, 1, 108, 108, 108, 108] 201
rigid atoms, others: [18, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54, 55, 56])
total number of confs: 932
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051689 none CCCCCCC(CC)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 13, 13, 6, 2, 6, 6, 2, 2, 1, 1, 1, 4, 11, 11, 11, 33, 48, 108, 108, 108, 108, 108, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 7, 7, 7, 7, 7, 2, 4, 4, 11, 33, 33, 108, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 53, 54, 55, 56, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 311
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051689 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051689
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051689/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051689
Building REAL300025051690
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051690'
/scratch/stefan/7786831/working/building/REAL300025051690 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051690

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051690/0 /scratch/stefan/7786831/working/building/REAL300025051690 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 565)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/565
`/scratch/stefan/7786831/working/3D/565' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC(N)=O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051690.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051690.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051690/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051690 none CC(CC(N)=O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 147, 201, 201, 201, 201, 147, 147, 147, 120, 83, 83, 33, 83, 13, 1, 1, 1, 1, 1, 1, 1, 147, 147, 201, 201, 201, 201, 201, 201, 201, 201, 147, 120, 120, 83, 33, 33, 1, 147, 147, 147, 147] 201
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42])
total number of confs: 859
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051690 none CC(CC(N)=O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 2, 6, 10, 28, 28, 2, 2, 1, 1, 1, 4, 10, 10, 10, 36, 56, 147, 147, 147, 147, 147, 1, 1, 6, 6, 6, 6, 10, 10, 28, 28, 2, 4, 4, 10, 36, 36, 147, 1, 1, 1, 1] 201
rigid atoms, others: [39, 8, 9, 10, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 388
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051690 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051690
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051690/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051690
Building REAL300025051691
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051691'
/scratch/stefan/7786831/working/building/REAL300025051691 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051691

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051691/0 /scratch/stefan/7786831/working/building/REAL300025051691 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 566)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/566
`/scratch/stefan/7786831/working/3D/566' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCNC2=O)CC1)

`REAL300025051691.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051691.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051691/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051691 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCNC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
199  conformations in input
total number of sets (complete confs): 199
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 77, 87, 178, 178, 178, 178, 178, 6, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 77, 77, 178, 24, 6, 6, 3, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1] 199
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 454
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051691 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCNC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
199  conformations in input
total number of sets (complete confs): 199
using faster count positions algorithm for large data
unique positions, atoms: [84, 35, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 153, 178, 178, 178, 178, 199, 199, 199, 199, 199, 178, 178, 35, 35, 1, 84, 153, 153, 178, 199, 199, 199, 199, 199, 199, 178, 178, 178, 178] 199
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 757
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051691 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCNC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
199  conformations in input
total number of sets (complete confs): 199
using faster count positions algorithm for large data
unique positions, atoms: [59, 59, 59, 128, 136, 199, 199, 199, 199, 199, 21, 13, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 13, 13, 128, 128, 199, 59, 21, 21, 9, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13] 199
rigid atoms, others: [32, 33, 34, 35, 36, 14, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40])
total number of confs: 613
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051691 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051691
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051691/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051691
Building REAL300025051692
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051692'
/scratch/stefan/7786831/working/building/REAL300025051692 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051692

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051692/0 /scratch/stefan/7786831/working/building/REAL300025051692 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 567)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/567
`/scratch/stefan/7786831/working/3D/567' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(=O)NC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051692.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051692.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051692/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051692 none CN1C(=O)NC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 8, 8, 8, 8, 2, 2, 2, 1, 1, 1, 4, 21, 21, 21, 66, 83, 149, 149, 149, 149, 149, 1, 1, 8, 8, 8, 8, 8, 2, 4, 4, 21, 66, 66, 149, 1, 1, 1, 1] 182
rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 390
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051692 none CN1C(=O)NC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 8, 8, 16, 61, 61, 61, 124, 142, 182, 182, 182, 182, 182, 8, 8, 2, 2, 2, 1, 1, 8, 16, 16, 61, 124, 124, 182, 8, 8, 8, 8] 182
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 580
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051692 none CN1C(=O)NC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [182, 182, 182, 182, 182, 182, 149, 149, 149, 149, 129, 79, 79, 35, 79, 13, 1, 1, 1, 1, 1, 1, 1, 149, 149, 182, 182, 182, 182, 182, 149, 129, 129, 79, 35, 35, 1, 149, 149, 149, 149] 182
rigid atoms, others: [36, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 623
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051692 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051692
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051692/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051692
Building REAL300025051693
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051693'
/scratch/stefan/7786831/working/building/REAL300025051693 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051693

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051693/0 /scratch/stefan/7786831/working/building/REAL300025051693 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 568)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/568
`/scratch/stefan/7786831/working/3D/568' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)NC1=O)

`REAL300025051693.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051693.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051693/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051693 none CN1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)NC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 29, 29, 29, 75, 94, 200, 200, 200, 200, 200, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 29, 75, 75, 200, 1, 1, 1, 1, 4] 201
rigid atoms, others: [6, 38, 7, 8, 41, 39, 40, 20, 21] set([0, 1, 2, 3, 4, 5, 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, 36, 37, 42])
total number of confs: 496
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051693 none CN1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)NC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 4, 15, 50, 50, 50, 112, 131, 201, 201, 201, 201, 201, 4, 4, 1, 1, 1, 2, 2, 2, 1, 1, 1, 4, 15, 15, 50, 112, 112, 201, 4, 4, 4, 4, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 42, 22, 23, 24, 28, 29, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 608
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051693 none CN1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)NC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 200, 200, 200, 200, 150, 68, 68, 29, 68, 13, 1, 1, 1, 1, 1, 1, 1, 200, 200, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 150, 150, 68, 29, 29, 1, 200, 200, 200, 200, 201] 201
rigid atoms, others: [37, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 770
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051693 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051693
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051693/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051693
Building REAL300025051694
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051694'
/scratch/stefan/7786831/working/building/REAL300025051694 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051694

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051694/0 /scratch/stefan/7786831/working/building/REAL300025051694 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 569)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/569
`/scratch/stefan/7786831/working/3D/569' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCCCCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051694.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051694.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051694/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051694 none C#CCCCCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 163, 169, 163, 155, 68, 68, 68, 68, 61, 39, 39, 23, 39, 12, 1, 1, 1, 1, 1, 1, 1, 68, 68, 201, 199, 201, 169, 169, 169, 169, 169, 169, 155, 155, 68, 61, 61, 39, 23, 23, 1, 68, 68, 68, 68] 201
rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46])
total number of confs: 955
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051694 none C#CCCCCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 38, 16, 19, 16, 10, 2, 2, 2, 1, 1, 1, 4, 6, 6, 6, 18, 24, 68, 68, 68, 68, 68, 1, 1, 38, 37, 36, 19, 19, 19, 19, 19, 19, 10, 10, 2, 4, 4, 6, 18, 18, 68, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 46, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 340
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051694 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051694
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051694/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051694
Building REAL300025051695
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051695'
/scratch/stefan/7786831/working/building/REAL300025051695 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300025051695

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051695/0 /scratch/stefan/7786831/working/building/REAL300025051695 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 570)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/570
`/scratch/stefan/7786831/working/3D/570' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@@H+]1CCC[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051695.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051695.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051695/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051695 none C[N@@H+]1CCC[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 3, 4, 4, 4, 10, 11, 12, 12, 12, 12, 12, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 4, 10, 10, 12, 1, 1, 1, 1] 12
rigid atoms, others: [43, 44, 10, 11, 12, 45, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
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: REAL300025051695 none C[N@@H+]1CCC[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 2, 2, 2, 2, 3, 4, 4, 4, 10, 11, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 3, 3, 4, 10, 10, 12, 2, 2, 2, 2] 12
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 33, 29, 30, 31] set([9, 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, 43, 44, 45])
total number of confs: 49
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051695 none C[N@@H+]1CCC[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 10, 12, 9, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 10, 10, 1, 12, 12, 12, 12] 12
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 24
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051695 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051695/1 /scratch/stefan/7786831/working/building/REAL300025051695 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 571)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/571
`/scratch/stefan/7786831/working/3D/571' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@H+]1CCC[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051695.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051695.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051695/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051695 none C[N@H+]1CCC[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 5, 5, 5, 2, 5, 2, 2, 1, 1, 1, 4, 8, 8, 8, 18, 23, 32, 32, 32, 32, 32, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 8, 18, 18, 32, 1, 1, 1, 1] 34
rigid atoms, others: [43, 44, 10, 11, 12, 45, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
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: REAL300025051695 none C[N@H+]1CCC[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 14, 14, 14, 25, 29, 34, 34, 34, 34, 34, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 10, 10, 14, 25, 25, 34, 5, 5, 5, 5] 34
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 33, 29, 30, 31] set([9, 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, 43, 44, 45])
total number of confs: 127
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051695 none C[N@H+]1CCC[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 32, 34, 32, 32, 32, 30, 27, 27, 19, 27, 12, 1, 1, 1, 1, 1, 1, 1, 32, 32, 34, 34, 34, 34, 34, 34, 34, 34, 34, 32, 30, 30, 27, 19, 19, 1, 32, 32, 32, 32] 34
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 116
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051695 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `2'
/scratch/stefan/7786831/working/building/REAL300025051695/2 /scratch/stefan/7786831/working/building/REAL300025051695 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 2 (index: 572)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/572
`/scratch/stefan/7786831/working/3D/572' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CCC[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051695.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300025051695.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051695/2/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`2.mol2' -> `2.mol2.original'
`output.mol2' -> `2.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051695 none CN1CCC[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 4, 2, 4, 2, 2, 1, 1, 1, 7, 25, 25, 25, 96, 133, 190, 190, 190, 190, 190, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 25, 96, 96, 190, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 527
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051695 none CN1CCC[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 15, 53, 53, 53, 135, 166, 201, 201, 201, 201, 201, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 15, 15, 53, 135, 135, 201, 4, 4, 4, 4] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 33, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 640
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051695 none CN1CCC[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 201, 190, 190, 190, 160, 77, 77, 27, 77, 12, 1, 1, 1, 1, 1, 1, 1, 190, 190, 201, 201, 201, 201, 201, 201, 201, 201, 201, 190, 160, 160, 77, 27, 27, 1, 190, 190, 190, 190] 201
rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 750
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051695 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051695
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
2: /scratch/stefan/7786831/working/building/REAL300025051695/2.*
1: /scratch/stefan/7786831/working/building/REAL300025051695/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051695/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051695
Building REAL300025051696
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051696'
/scratch/stefan/7786831/working/building/REAL300025051696 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051696

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051696/0 /scratch/stefan/7786831/working/building/REAL300025051696 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 573)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/573
`/scratch/stefan/7786831/working/3D/573' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1C[C@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051696.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051696.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051696/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051696 none C[C@@H]1C[C@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 11, 2, 11, 2, 2, 1, 1, 1, 4, 17, 17, 17, 52, 70, 150, 150, 150, 150, 150, 1, 1, 11, 11, 11, 11, 11, 2, 4, 4, 17, 52, 52, 150, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 360
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051696 none C[C@@H]1C[C@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 22, 57, 57, 57, 120, 147, 201, 201, 201, 201, 201, 11, 11, 2, 2, 2, 1, 1, 11, 22, 22, 57, 120, 120, 201, 11, 11, 11, 11] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 623
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051696 none C[C@@H]1C[C@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 150, 201, 150, 150, 150, 125, 74, 74, 31, 74, 13, 1, 1, 1, 1, 1, 1, 1, 150, 150, 201, 201, 201, 201, 201, 150, 125, 125, 74, 31, 31, 1, 150, 150, 150, 150] 201
rigid atoms, others: [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, 33, 34, 36, 37, 38, 39])
total number of confs: 749
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051696 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051696
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051696/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051696
Building REAL300025051697
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051697'
/scratch/stefan/7786831/working/building/REAL300025051697 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051697

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051697/0 /scratch/stefan/7786831/working/building/REAL300025051697 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 574)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/574
`/scratch/stefan/7786831/working/3D/574' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CC=CCC2)CC1)

`REAL300025051697.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051697.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051697/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051697 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CC=CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 14, 14, 31, 33, 70, 70, 70, 70, 70, 5, 1, 1, 1, 3, 3, 3, 19, 45, 45, 45, 45, 45, 1, 1, 31, 31, 70, 14, 5, 5, 3, 19, 19, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1] 201
rigid atoms, others: [11, 44, 43, 12, 13, 46, 45, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 326
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051697 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CC=CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 21, 13, 1, 1, 1, 1, 1, 1, 1, 32, 32, 60, 70, 70, 70, 70, 179, 201, 201, 201, 201, 201, 70, 70, 21, 21, 1, 32, 60, 60, 70, 179, 179, 201, 201, 201, 201, 201, 201, 201, 201, 201, 70, 70, 70, 70] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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, 45, 46])
total number of confs: 814
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051697 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CC=CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [128, 128, 128, 187, 191, 201, 201, 201, 201, 201, 61, 45, 25, 25, 6, 25, 1, 1, 1, 1, 1, 1, 1, 45, 45, 187, 187, 201, 128, 61, 61, 25, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46])
total number of confs: 800
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051697 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051697
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051697/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051697
Building REAL300025051698
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051698'
/scratch/stefan/7786831/working/building/REAL300025051698 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051698

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051698/0 /scratch/stefan/7786831/working/building/REAL300025051698 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 575)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/575
`/scratch/stefan/7786831/working/3D/575' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(F)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051698.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051698.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051698/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051698 none CCC(F)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 192, 180, 192, 180, 180, 180, 146, 63, 63, 23, 63, 13, 1, 1, 1, 1, 1, 1, 1, 180, 180, 201, 201, 201, 201, 201, 192, 180, 146, 146, 63, 23, 23, 1, 180, 180, 180, 180] 201
rigid atoms, others: [34, 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, 35, 36, 37, 38])
total number of confs: 810
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051698 none CCC(F)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 6, 2, 6, 2, 2, 1, 1, 1, 4, 18, 18, 18, 81, 105, 180, 180, 180, 180, 180, 1, 1, 8, 8, 8, 8, 8, 6, 2, 4, 4, 18, 81, 81, 180, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 6, 7, 8, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 490
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051698 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051698
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051698/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051698
Building REAL300025051699
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051699'
/scratch/stefan/7786831/working/building/REAL300025051699 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051699

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051699/0 /scratch/stefan/7786831/working/building/REAL300025051699 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 576)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/576
`/scratch/stefan/7786831/working/3D/576' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCF)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051699.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051699.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051699/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051699 none O=C(CCCF)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [135, 135, 135, 196, 200, 201, 135, 120, 69, 69, 30, 69, 13, 1, 1, 1, 1, 1, 1, 1, 135, 135, 196, 196, 201, 201, 201, 201, 135, 120, 120, 69, 30, 30, 1, 135, 135, 135, 135] 201
rigid atoms, others: [34, 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, 35, 36, 37, 38])
total number of confs: 860
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051699 none O=C(CCCF)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 10, 16, 27, 1, 1, 1, 6, 15, 15, 15, 41, 63, 135, 135, 135, 135, 135, 1, 1, 10, 10, 20, 20, 25, 25, 2, 6, 6, 15, 41, 41, 135, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 6, 7, 8, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 434
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051699 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051699
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051699/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051699
Building REAL300025051700
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051700'
/scratch/stefan/7786831/working/building/REAL300025051700 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051700

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051700/0 /scratch/stefan/7786831/working/building/REAL300025051700 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 577)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/577
`/scratch/stefan/7786831/working/3D/577' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C(F)(F)F)

`REAL300025051700.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051700.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051700/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051700 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C(F)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 167, 167, 167, 167, 148, 82, 82, 33, 82, 13, 1, 1, 1, 1, 1, 1, 1, 167, 167, 201, 201, 201, 201, 201, 201, 201, 201, 167, 148, 148, 82, 33, 33, 1, 167, 167, 167, 167] 201
rigid atoms, others: [34, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 802
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051700 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C(F)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 2, 2, 2, 1, 1, 1, 4, 19, 19, 19, 72, 98, 167, 167, 167, 167, 167, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 2, 4, 4, 19, 72, 72, 167, 1, 1, 1, 1] 201
rigid atoms, others: [35, 4, 5, 6, 18, 19, 36, 38, 37] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 442
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051700 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051700
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051700/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051700
Building REAL300025051701
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051701'
/scratch/stefan/7786831/working/building/REAL300025051701 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051701

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051701/0 /scratch/stefan/7786831/working/building/REAL300025051701 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 578)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/578
`/scratch/stefan/7786831/working/3D/578' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=COC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051701.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051701.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051701/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051701 none CC1=COC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 4, 22, 22, 22, 81, 100, 174, 174, 174, 174, 174, 1, 1, 7, 7, 7, 7, 7, 2, 4, 4, 22, 81, 81, 174, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 450
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051701 none CC1=COC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 18, 57, 57, 57, 134, 152, 201, 201, 201, 201, 201, 7, 7, 2, 2, 2, 1, 1, 7, 18, 18, 57, 134, 134, 201, 7, 7, 7, 7] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 624
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051701 none CC1=COC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 174, 174, 174, 174, 147, 78, 78, 32, 78, 13, 1, 1, 1, 1, 1, 1, 1, 174, 174, 201, 201, 201, 201, 201, 174, 147, 147, 78, 32, 32, 1, 174, 174, 174, 174] 201
rigid atoms, others: [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, 33, 34, 36, 37, 38, 39])
total number of confs: 716
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051701 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051701
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051701/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051701
Building REAL300025051702
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051702'
/scratch/stefan/7786831/working/building/REAL300025051702 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051702

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051702/0 /scratch/stefan/7786831/working/building/REAL300025051702 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 579)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/579
`/scratch/stefan/7786831/working/3D/579' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H]1C[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051702.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051702.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051702/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051702 none C[C@H]1C[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 11, 2, 11, 2, 2, 1, 1, 1, 4, 16, 16, 16, 48, 63, 136, 136, 136, 136, 136, 1, 1, 11, 11, 11, 11, 11, 2, 4, 4, 16, 48, 48, 136, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
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: REAL300025051702 none C[C@H]1C[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 22, 57, 57, 57, 121, 143, 201, 201, 201, 201, 201, 11, 11, 2, 2, 2, 1, 1, 11, 22, 22, 57, 121, 121, 201, 11, 11, 11, 11] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 627
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051702 none C[C@H]1C[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 136, 201, 136, 136, 136, 119, 71, 71, 32, 71, 12, 1, 1, 1, 1, 1, 1, 1, 136, 136, 201, 201, 201, 201, 201, 136, 119, 119, 71, 32, 32, 1, 136, 136, 136, 136] 201
rigid atoms, others: [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, 33, 34, 36, 37, 38, 39])
total number of confs: 762
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051702 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051702
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051702/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051702
Building REAL300025051703
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051703'
/scratch/stefan/7786831/working/building/REAL300025051703 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051703

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051703/0 /scratch/stefan/7786831/working/building/REAL300025051703 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 580)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/580
`/scratch/stefan/7786831/working/3D/580' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1)

`REAL300025051703.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051703.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051703/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051703 none CN1N=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 7, 26, 26, 26, 87, 105, 186, 186, 186, 186, 186, 1, 1, 5, 5, 5, 5, 2, 7, 7, 26, 87, 87, 186, 1, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 490
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051703 none CN1N=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 15, 41, 41, 41, 108, 126, 201, 201, 201, 201, 201, 5, 5, 1, 2, 2, 2, 5, 15, 15, 41, 108, 108, 201, 5, 5, 5, 5] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 23] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 572
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051703 none CN1N=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 186, 186, 186, 186, 140, 68, 68, 30, 68, 13, 1, 1, 1, 1, 1, 1, 1, 186, 186, 201, 201, 201, 201, 186, 140, 140, 68, 30, 30, 1, 186, 186, 186, 186] 201
rigid atoms, others: [33, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 733
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051703 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051703
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051703/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051703
Building REAL300025051704
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051704'
/scratch/stefan/7786831/working/building/REAL300025051704 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051704

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051704/0 /scratch/stefan/7786831/working/building/REAL300025051704 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 581)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/581
`/scratch/stefan/7786831/working/3D/581' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051704.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051704.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051704/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051704 none CC1(C)CCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 4, 18, 18, 18, 62, 70, 106, 106, 106, 106, 106, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 18, 62, 62, 106, 1, 1, 1, 1] 107
rigid atoms, others: [9, 10, 11, 45, 46, 47, 48, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 310
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: REAL300025051704 none CC1(C)CCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 20, 20, 20, 64, 71, 107, 107, 107, 107, 107, 3, 3, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 20, 64, 64, 107, 3, 3, 3, 3] 107
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 35, 36, 33, 37, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 323
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051704 none CC1(C)CCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [107, 107, 107, 107, 107, 107, 106, 106, 106, 106, 97, 60, 60, 30, 60, 13, 1, 1, 1, 1, 1, 1, 1, 106, 106, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 106, 97, 97, 60, 30, 30, 1, 106, 106, 106, 106] 107
rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48])
total number of confs: 416
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051704 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051704
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051704/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051704
Building REAL300025051705
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051705'
/scratch/stefan/7786831/working/building/REAL300025051705 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051705

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051705/0 /scratch/stefan/7786831/working/building/REAL300025051705 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 582)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/582
`/scratch/stefan/7786831/working/3D/582' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCCCN3C=C2)CC1)

`REAL300025051705.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051705.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051705/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051705 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCCCN3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 82, 97, 190, 190, 190, 190, 190, 6, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 82, 82, 190, 24, 6, 6, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1] 201
rigid atoms, others: [44, 11, 12, 13, 46, 45, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 478
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051705 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCCCN3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [77, 34, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 145, 190, 190, 190, 190, 201, 201, 201, 201, 201, 201, 201, 201, 190, 190, 34, 34, 1, 77, 145, 145, 190, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 190, 190, 190, 190] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46, 47])
total number of confs: 720
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051705 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCCCN3C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 144, 154, 201, 201, 201, 201, 201, 17, 10, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 144, 144, 201, 57, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 44, 45, 46, 47])
total number of confs: 674
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051705 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051705
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051705/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051705
Building REAL300025051706
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051706'
/scratch/stefan/7786831/working/building/REAL300025051706 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051706

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051706/0 /scratch/stefan/7786831/working/building/REAL300025051706 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 583)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/583
`/scratch/stefan/7786831/working/3D/583' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(COCC1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051706.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051706.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051706/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051706 none O=C(COCC1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 4, 9, 14, 32, 32, 32, 32, 1, 1, 1, 3, 9, 9, 9, 25, 31, 66, 66, 66, 66, 66, 1, 1, 4, 4, 14, 14, 32, 32, 32, 32, 32, 32, 32, 32, 32, 2, 3, 3, 9, 25, 25, 66, 1, 1, 1, 1] 201
rigid atoms, others: [10, 11, 12, 46, 47, 48, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 255
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051706 none O=C(COCC1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 22, 13, 5, 1, 1, 1, 1, 1, 1, 32, 32, 32, 49, 65, 65, 65, 125, 150, 201, 201, 201, 201, 201, 32, 32, 22, 22, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 49, 49, 65, 125, 125, 201, 32, 32, 32, 32] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 36, 38, 37, 30, 31] set([0, 1, 2, 3, 10, 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])
total number of confs: 688
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051706 none O=C(COCC1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [66, 66, 66, 100, 132, 143, 201, 201, 201, 201, 66, 56, 46, 46, 37, 46, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 100, 100, 143, 143, 201, 201, 201, 201, 201, 201, 201, 201, 201, 66, 56, 56, 46, 37, 37, 1, 66, 66, 66, 66] 201
rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49])
total number of confs: 767
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051706 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051706
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051706/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051706
Building REAL300025051707
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051707'
/scratch/stefan/7786831/working/building/REAL300025051707 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051707

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051707/0 /scratch/stefan/7786831/working/building/REAL300025051707 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 584)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/584
`/scratch/stefan/7786831/working/3D/584' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=C(Cl)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NN1)

`REAL300025051707.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051707.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051707/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051707 none CCC1=C(Cl)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 4, 16, 16, 16, 45, 50, 99, 99, 99, 99, 99, 1, 1, 3, 3, 6, 6, 6, 6, 6, 2, 4, 4, 16, 45, 45, 99, 1, 1, 1, 1, 3] 201
rigid atoms, others: [38, 39, 8, 9, 10, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 42])
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: REAL300025051707 none CCC1=C(Cl)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
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, 3, 3, 3, 3, 7, 26, 26, 26, 59, 64, 112, 112, 112, 112, 112, 3, 3, 1, 1, 4, 4, 4, 4, 4, 3, 7, 7, 26, 59, 59, 112, 3, 3, 3, 3, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 42, 24, 25] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 330
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051707 none CCC1=C(Cl)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 112, 112, 112, 112, 99, 99, 99, 99, 83, 51, 51, 31, 51, 13, 1, 1, 1, 1, 1, 1, 1, 99, 99, 112, 112, 201, 201, 201, 201, 201, 99, 83, 83, 51, 31, 31, 1, 99, 99, 99, 99, 112] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 940
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051707 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051707/1 /scratch/stefan/7786831/working/building/REAL300025051707 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 585)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/585
`/scratch/stefan/7786831/working/3D/585' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1Cl)

`REAL300025051707.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051707.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051707/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051707 none CCC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'Cl', '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, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 16, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 6, 19, 19, 19, 55, 70, 101, 101, 101, 101, 101, 1, 1, 4, 4, 7, 7, 7, 7, 7, 4, 2, 6, 6, 19, 55, 55, 101, 1, 1, 1, 1] 201
rigid atoms, others: [39, 8, 9, 10, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 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: REAL300025051707 none CCC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'Cl', '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, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 16, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 25, 25, 25, 64, 82, 111, 111, 111, 111, 111, 4, 4, 1, 1, 3, 3, 3, 2, 2, 1, 4, 10, 10, 25, 64, 64, 111, 4, 4, 4, 4] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 24, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 339
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051707 none CCC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'Cl', '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, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 16, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 111, 111, 111, 111, 101, 101, 101, 101, 92, 58, 58, 26, 58, 13, 1, 1, 1, 1, 1, 1, 1, 101, 101, 111, 111, 201, 201, 201, 201, 201, 111, 101, 92, 92, 58, 26, 26, 1, 101, 101, 101, 101] 201
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42])
total number of confs: 948
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051707 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051707
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051707/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051707/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051707
Building REAL300025051708
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051708'
/scratch/stefan/7786831/working/building/REAL300025051708 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051708

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051708/0 /scratch/stefan/7786831/working/building/REAL300025051708 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 586)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/586
`/scratch/stefan/7786831/working/3D/586' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=CC3=CC=CN=C32)CC1)

`REAL300025051708.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051708.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051708/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051708 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=CC3=CC=CN=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 62, 73, 161, 161, 161, 161, 161, 6, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 62, 62, 161, 20, 6, 6, 3, 13, 13, 13, 13, 13, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
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: REAL300025051708 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=CC3=CC=CN=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 34, 13, 1, 1, 1, 1, 1, 1, 1, 68, 68, 134, 161, 161, 161, 161, 201, 201, 201, 201, 201, 201, 201, 201, 201, 161, 161, 34, 34, 1, 68, 134, 134, 161, 201, 201, 201, 201, 201, 161, 161, 161, 161] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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])
total number of confs: 686
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051708 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=CC3=CC=CN=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 61, 61, 132, 144, 201, 201, 201, 201, 201, 22, 13, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 132, 132, 201, 61, 22, 22, 8, 1, 1, 1, 1, 1, 13, 13, 13, 13] 201
rigid atoms, others: [35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43])
total number of confs: 630
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051708 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051708
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051708/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051708
Building REAL300025051709
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051709'
/scratch/stefan/7786831/working/building/REAL300025051709 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051709

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051709/0 /scratch/stefan/7786831/working/building/REAL300025051709 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 587)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/587
`/scratch/stefan/7786831/working/3D/587' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C(C3CC3)O2)CC1)

`REAL300025051709.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051709.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051709/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051709 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C(C3CC3)O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 15, 39, 44, 109, 109, 109, 109, 109, 5, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 44, 44, 11, 1, 1, 39, 39, 109, 15, 5, 5, 3, 11, 44, 44, 44, 44, 44, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 348
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051709 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C(C3CC3)O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [45, 29, 13, 1, 1, 1, 1, 1, 1, 1, 45, 45, 84, 109, 109, 109, 109, 132, 132, 132, 132, 201, 201, 132, 109, 109, 29, 29, 1, 45, 84, 84, 109, 132, 201, 201, 201, 201, 201, 109, 109, 109, 109] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 744
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051709 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C(C3CC3)O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [121, 121, 121, 168, 172, 201, 201, 201, 201, 201, 60, 44, 30, 30, 13, 30, 12, 12, 13, 1, 1, 1, 1, 13, 44, 44, 168, 168, 201, 121, 60, 60, 30, 13, 1, 1, 1, 1, 1, 44, 44, 44, 44] 201
rigid atoms, others: [34, 35, 36, 37, 38, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42])
total number of confs: 734
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051709 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C(C3CC3)O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 31, 31, 63, 68, 132, 132, 132, 132, 132, 14, 11, 7, 6, 1, 6, 1, 1, 1, 1, 1, 13, 13, 1, 11, 11, 63, 63, 132, 31, 14, 14, 7, 1, 12, 13, 13, 13, 13, 11, 11, 11, 11] 201
rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 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
/scratch/stefan/7786831/working/building/REAL300025051709 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051709
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051709/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051709
Building REAL300025051710
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051710'
/scratch/stefan/7786831/working/building/REAL300025051710 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051710

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051710/0 /scratch/stefan/7786831/working/building/REAL300025051710 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 588)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/588
`/scratch/stefan/7786831/working/3D/588' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C[C@@H]2NC(=O)NC2=O)CC1)

`REAL300025051710.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051710.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051710/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051710 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C[C@@H]2NC(=O)NC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 7, 8, 1, 11, 8, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 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: [12, 12, 12, 22, 28, 68, 68, 68, 68, 68, 5, 1, 1, 1, 3, 3, 3, 21, 55, 55, 55, 55, 55, 55, 55, 1, 1, 22, 22, 68, 12, 5, 5, 3, 21, 21, 55, 55, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051710 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C[C@@H]2NC(=O)NC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 7, 8, 1, 11, 8, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 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: [41, 24, 13, 1, 1, 1, 1, 1, 1, 1, 41, 41, 61, 68, 68, 68, 68, 168, 201, 201, 201, 201, 201, 201, 201, 68, 68, 24, 24, 1, 41, 61, 61, 68, 168, 168, 201, 201, 68, 68, 68, 68] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 794
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051710 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C[C@@H]2NC(=O)NC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 7, 8, 1, 11, 8, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 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: [132, 132, 132, 167, 174, 201, 201, 201, 201, 201, 71, 55, 40, 40, 10, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 167, 167, 201, 132, 71, 71, 40, 10, 10, 1, 1, 55, 55, 55, 55] 201
rigid atoms, others: [36, 37, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41])
total number of confs: 707
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051710 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051710
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051710/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051710
Building REAL300025051711
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051711'
/scratch/stefan/7786831/working/building/REAL300025051711 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051711

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051711/0 /scratch/stefan/7786831/working/building/REAL300025051711 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 589)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/589
`/scratch/stefan/7786831/working/3D/589' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051711.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051711.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051711/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051711 none COCC1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [27, 14, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 6, 9, 9, 9, 12, 19, 67, 67, 67, 67, 67, 1, 1, 3, 27, 27, 27, 14, 14, 3, 3, 2, 6, 6, 9, 12, 12, 67, 1, 1, 1, 1, 3] 120
rigid atoms, others: [43, 41, 10, 11, 12, 44, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45])
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: REAL300025051711 none COCC1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [19, 9, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 8, 11, 11, 11, 16, 25, 82, 82, 82, 82, 82, 3, 3, 1, 19, 19, 19, 9, 9, 1, 1, 3, 8, 8, 11, 16, 16, 82, 3, 3, 3, 3, 1] 120
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 45, 26] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 200
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051711 none COCC1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [120, 120, 82, 82, 82, 82, 82, 67, 67, 67, 67, 56, 53, 53, 33, 53, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 82, 120, 120, 120, 120, 120, 82, 82, 67, 56, 56, 53, 33, 33, 1, 67, 67, 67, 67, 82] 120
rigid atoms, others: [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, 37, 38, 39, 41, 42, 43, 44, 45])
total number of confs: 485
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051711 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051711
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051711/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051711
Building REAL300025051712
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051712'
/scratch/stefan/7786831/working/building/REAL300025051712 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051712

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051712/0 /scratch/stefan/7786831/working/building/REAL300025051712 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 590)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/590
`/scratch/stefan/7786831/working/3D/590' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3CCCN23)CC1)

`REAL300025051712.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051712.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051712/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051712 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3CCCN23)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', '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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 28, 28, 91, 111, 193, 193, 193, 193, 193, 6, 1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 1, 1, 91, 91, 193, 28, 6, 6, 3, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 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: REAL300025051712 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3CCCN23)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', '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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [74, 36, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 142, 193, 193, 193, 193, 201, 201, 201, 201, 201, 201, 201, 193, 193, 36, 36, 1, 74, 142, 142, 193, 201, 201, 201, 201, 201, 201, 201, 193, 193, 193, 193] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 717
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051712 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3CCCN23)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', '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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 61, 61, 140, 152, 201, 201, 201, 201, 201, 20, 12, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 140, 140, 201, 61, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43])
total number of confs: 682
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051712 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051712
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051712/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051712
Building REAL300025051713
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051713'
/scratch/stefan/7786831/working/building/REAL300025051713 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051713

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051713/0 /scratch/stefan/7786831/working/building/REAL300025051713 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 591)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/591
`/scratch/stefan/7786831/working/3D/591' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=NC=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051713.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051713.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051713/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051713 none CC1=CC=NC=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 20, 20, 20, 20, 13, 2, 2, 2, 1, 1, 1, 6, 13, 13, 13, 34, 45, 117, 117, 117, 117, 117, 1, 1, 20, 20, 20, 20, 20, 20, 13, 13, 2, 6, 6, 13, 34, 34, 117, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 10, 11, 12, 44, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
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: REAL300025051713 none CC1=CC=NC=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 20, 20, 20, 20, 36, 50, 50, 50, 92, 116, 201, 201, 201, 201, 201, 20, 20, 2, 2, 2, 1, 1, 1, 5, 5, 20, 36, 36, 50, 92, 92, 201, 20, 20, 20, 20] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29, 30, 31] set([8, 9, 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, 41, 42, 43, 44])
total number of confs: 609
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051713 none CC1=CC=NC=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 187, 117, 117, 117, 117, 95, 51, 51, 26, 51, 13, 1, 1, 1, 1, 1, 1, 1, 117, 117, 201, 201, 201, 201, 201, 201, 187, 187, 117, 95, 95, 51, 26, 26, 1, 117, 117, 117, 117] 201
rigid atoms, others: [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, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 811
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051713 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051713
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051713/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051713
Building REAL300025051714
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051714'
/scratch/stefan/7786831/working/building/REAL300025051714 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051714

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051714/0 /scratch/stefan/7786831/working/building/REAL300025051714 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 592)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/592
`/scratch/stefan/7786831/working/3D/592' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1OCCO[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051714.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051714.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051714/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051714 none C[C@@H]1OCCO[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 2, 3, 2, 2, 1, 1, 1, 7, 25, 25, 25, 89, 124, 197, 197, 197, 197, 197, 1, 1, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 25, 89, 89, 197, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 42, 11, 12, 13, 44, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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])
total number of confs: 525
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051714 none C[C@@H]1OCCO[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 12, 37, 37, 37, 102, 135, 201, 201, 201, 201, 201, 3, 3, 2, 2, 2, 1, 1, 1, 1, 3, 12, 12, 37, 102, 102, 201, 3, 3, 3, 3] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 33, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 565
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051714 none C[C@@H]1OCCO[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 197, 201, 197, 197, 197, 172, 90, 90, 28, 90, 12, 1, 1, 1, 1, 1, 1, 1, 197, 197, 201, 201, 201, 201, 201, 201, 201, 197, 172, 172, 90, 28, 28, 1, 197, 197, 197, 197] 201
rigid atoms, others: [40, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 752
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051714 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051714
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051714/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051714
Building REAL300025051715
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051715'
/scratch/stefan/7786831/working/building/REAL300025051715 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051715

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051715/0 /scratch/stefan/7786831/working/building/REAL300025051715 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 593)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/593
`/scratch/stefan/7786831/working/3D/593' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC1=O)

`REAL300025051715.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051715.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051715/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051715 none CN1C=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 28, 28, 28, 96, 119, 198, 199, 199, 199, 199, 1, 1, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 28, 96, 96, 199, 1, 1, 1, 1, 4] 201
rigid atoms, others: [37, 38, 7, 8, 9, 39, 40, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 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, 41])
total number of confs: 541
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051715 none CN1C=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 11, 38, 38, 38, 111, 132, 200, 201, 201, 201, 201, 4, 4, 1, 1, 1, 2, 2, 2, 1, 4, 11, 11, 38, 111, 111, 201, 4, 4, 4, 4, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 23, 24, 25, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 588
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051715 none CN1C=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 199, 199, 199, 199, 142, 66, 66, 30, 66, 13, 1, 1, 1, 1, 1, 1, 1, 199, 199, 201, 201, 201, 201, 201, 201, 201, 199, 142, 142, 66, 30, 30, 1, 199, 199, 199, 199, 201] 201
rigid atoms, others: [36, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41])
total number of confs: 754
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051715 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051715
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051715/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051715
Building REAL300025051716
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051716'
/scratch/stefan/7786831/working/building/REAL300025051716 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051716

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051716/0 /scratch/stefan/7786831/working/building/REAL300025051716 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 594)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/594
`/scratch/stefan/7786831/working/3D/594' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CNC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1)

`REAL300025051716.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051716.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051716/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051716 none CCC1=CNC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 6, 6, 5, 2, 2, 2, 1, 1, 1, 4, 9, 9, 9, 29, 47, 105, 105, 105, 105, 105, 1, 1, 6, 18, 18, 18, 18, 18, 6, 6, 5, 5, 2, 4, 4, 9, 29, 29, 105, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
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: REAL300025051716 none CCC1=CNC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 4, 6, 6, 6, 6, 13, 19, 19, 19, 52, 73, 129, 129, 129, 129, 129, 6, 6, 1, 6, 6, 6, 6, 6, 1, 1, 4, 4, 6, 13, 13, 19, 52, 52, 129, 6, 6, 6, 6] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 368
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051716 none CCC1=CNC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 129, 129, 129, 129, 129, 105, 105, 105, 105, 99, 74, 74, 52, 74, 13, 1, 1, 1, 1, 1, 1, 1, 105, 105, 129, 201, 201, 201, 201, 201, 129, 129, 129, 129, 105, 99, 99, 74, 52, 52, 1, 105, 105, 105, 105] 201
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 979
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051716 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051716
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051716/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051716
Building REAL300025051717
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051717'
/scratch/stefan/7786831/working/building/REAL300025051717 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051717

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051717/0 /scratch/stefan/7786831/working/building/REAL300025051717 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 595)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/595
`/scratch/stefan/7786831/working/3D/595' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@@H+]1CCCC1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051717.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051717.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051717/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051717 none C[N@@H+]1CCCC1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 6, 6, 6, 6, 4, 5, 2, 2, 2, 1, 1, 1, 5, 7, 7, 7, 12, 16, 23, 23, 23, 23, 23, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 2, 5, 5, 7, 12, 12, 23, 1, 1, 1, 1] 24
rigid atoms, others: [11, 12, 13, 48, 49, 50, 51, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 90
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051717 none C[N@@H+]1CCCC1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 5, 6, 6, 6, 6, 7, 8, 8, 8, 13, 17, 24, 24, 24, 24, 24, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 6, 7, 7, 8, 13, 13, 24, 6, 6, 6, 6] 24
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 35, 36, 33, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 82
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051717 none C[N@@H+]1CCCC1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 23, 24, 23, 23, 23, 23, 20, 19, 19, 16, 19, 11, 1, 1, 1, 1, 1, 1, 1, 23, 23, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 23, 20, 20, 19, 16, 16, 1, 23, 23, 23, 23] 24
rigid atoms, others: [47, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51])
total number of confs: 83
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051717 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051717/1 /scratch/stefan/7786831/working/building/REAL300025051717 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 596)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/596
`/scratch/stefan/7786831/working/3D/596' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@H+]1CCCC1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051717.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051717.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051717/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051717 none C[N@H+]1CCCC1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
6  conformations in input
total number of sets (complete confs): 6
using default count positions algorithm for smaller data
unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 6, 1, 1, 1, 1] 6
rigid atoms, others: [11, 12, 13, 48, 49, 50, 51, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 20
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: REAL300025051717 none C[N@H+]1CCCC1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 6, 2, 2, 2, 2] 6
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 35, 36, 33, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 22
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051717 none C[N@H+]1CCCC1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
6  conformations in input
total number of sets (complete confs): 6
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 1, 6, 6, 6, 6] 6
rigid atoms, others: [47, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51])
total number of confs: 17
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051717 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051717
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051717/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051717/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051717
Building REAL300025051718
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051718'
/scratch/stefan/7786831/working/building/REAL300025051718 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051718

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051718/0 /scratch/stefan/7786831/working/building/REAL300025051718 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 597)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/597
`/scratch/stefan/7786831/working/3D/597' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051718.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051718.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051718/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051718 none CC[C@@H]1CCO[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 2, 4, 2, 2, 1, 1, 1, 6, 22, 22, 22, 83, 126, 195, 195, 195, 195, 195, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 6, 6, 22, 83, 83, 195, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 506
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: REAL300025051718 none CC[C@@H]1CCO[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 32, 32, 32, 99, 139, 201, 201, 201, 201, 201, 4, 4, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 11, 11, 32, 99, 99, 201, 4, 4, 4, 4] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 33] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 559
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051718 none CC[C@@H]1CCO[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 195, 201, 195, 195, 195, 159, 91, 91, 29, 91, 12, 1, 1, 1, 1, 1, 1, 1, 195, 195, 201, 201, 201, 201, 201, 201, 201, 201, 201, 195, 159, 159, 91, 29, 29, 1, 195, 195, 195, 195] 201
rigid atoms, others: [42, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46])
total number of confs: 754
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051718 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051718
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051718/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051718
Building REAL300025051719
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051719'
/scratch/stefan/7786831/working/building/REAL300025051719 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051719

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051719/0 /scratch/stefan/7786831/working/building/REAL300025051719 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 598)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/598
`/scratch/stefan/7786831/working/3D/598' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2=CNC=N2)CC1)

`REAL300025051719.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051719.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051719/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051719 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2=CNC=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 15, 40, 45, 109, 109, 109, 109, 109, 5, 1, 1, 1, 3, 3, 3, 20, 20, 20, 20, 20, 65, 65, 65, 65, 1, 1, 40, 40, 109, 15, 5, 5, 3, 20, 20, 65, 65, 65, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 354
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051719 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2=CNC=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 12, 1, 1, 1, 1, 1, 1, 1, 51, 51, 95, 109, 109, 109, 109, 188, 188, 188, 188, 188, 201, 201, 201, 201, 109, 109, 30, 30, 1, 51, 95, 95, 109, 188, 188, 201, 201, 201, 109, 109, 109, 109] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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])
total number of confs: 708
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051719 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2=CNC=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [143, 143, 143, 182, 184, 201, 201, 201, 201, 201, 80, 65, 53, 53, 11, 53, 11, 11, 11, 1, 11, 1, 1, 1, 1, 1, 65, 65, 182, 182, 201, 143, 80, 80, 53, 11, 11, 1, 1, 1, 65, 65, 65, 65] 201
rigid atoms, others: [37, 38, 39, 19, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43])
total number of confs: 720
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051719 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2=CNC=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 142, 148, 188, 188, 188, 188, 188, 29, 20, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 20, 20, 142, 142, 188, 80, 29, 29, 12, 1, 1, 11, 11, 11, 20, 20, 20, 20] 201
rigid atoms, others: [35, 36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 668
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051719 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051719/1 /scratch/stefan/7786831/working/building/REAL300025051719 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 599)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/599
`/scratch/stefan/7786831/working/3D/599' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2=CN=CN2)CC1)

`REAL300025051719.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051719.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051719/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051719 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2=CN=CN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
169  conformations in input
total number of sets (complete confs): 169
using faster count positions algorithm for large data
unique positions, atoms: [14, 14, 14, 42, 48, 108, 108, 108, 108, 108, 5, 1, 1, 1, 3, 3, 3, 20, 20, 20, 20, 20, 63, 63, 63, 63, 1, 1, 42, 42, 108, 14, 5, 5, 3, 20, 20, 63, 63, 63, 1, 1, 1, 1] 169
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 358
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051719 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2=CN=CN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
169  conformations in input
total number of sets (complete confs): 169
using faster count positions algorithm for large data
unique positions, atoms: [53, 31, 13, 1, 1, 1, 1, 1, 1, 1, 53, 53, 93, 108, 108, 108, 108, 162, 162, 162, 162, 162, 169, 169, 169, 169, 108, 108, 31, 31, 1, 53, 93, 93, 108, 162, 162, 169, 169, 169, 108, 108, 108, 108] 169
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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])
total number of confs: 631
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051719 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2=CN=CN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
169  conformations in input
total number of sets (complete confs): 169
using faster count positions algorithm for large data
unique positions, atoms: [125, 125, 125, 163, 163, 169, 169, 169, 169, 169, 79, 63, 55, 55, 13, 55, 13, 13, 13, 1, 13, 1, 1, 1, 1, 1, 63, 63, 163, 163, 169, 125, 79, 79, 55, 13, 13, 1, 1, 1, 63, 63, 63, 63] 169
rigid atoms, others: [37, 38, 39, 19, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43])
total number of confs: 622
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051719 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2=CN=CN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
169  conformations in input
total number of sets (complete confs): 169
using faster count positions algorithm for large data
unique positions, atoms: [80, 80, 80, 137, 141, 162, 162, 162, 162, 162, 30, 20, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 20, 20, 137, 137, 162, 80, 30, 30, 12, 1, 1, 13, 13, 13, 20, 20, 20, 20] 169
rigid atoms, others: [35, 36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 627
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051719 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051719
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051719/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051719/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051719
Building REAL300025051720
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051720'
/scratch/stefan/7786831/working/building/REAL300025051720 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051720

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051720/0 /scratch/stefan/7786831/working/building/REAL300025051720 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 600)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/600
`/scratch/stefan/7786831/working/3D/600' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3COCCN23)CC1)

`REAL300025051720.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051720.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051720/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051720 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3COCCN23)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', '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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 12, 5, 5, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 26, 94, 112, 198, 198, 198, 198, 198, 6, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 94, 94, 198, 26, 6, 6, 3, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 42, 11, 12, 13, 44, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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])
total number of confs: 521
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051720 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3COCCN23)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', '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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 12, 5, 5, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 146, 198, 198, 198, 198, 201, 201, 201, 201, 201, 201, 201, 201, 198, 198, 32, 32, 1, 67, 146, 146, 198, 201, 201, 201, 201, 201, 201, 201, 198, 198, 198, 198] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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: 750
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051720 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3COCCN23)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', '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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 12, 5, 5, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 134, 148, 201, 201, 201, 201, 201, 15, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 134, 134, 201, 57, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44])
total number of confs: 640
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051720 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051720
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051720/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051720
Building REAL300025051721
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051721'
/scratch/stefan/7786831/working/building/REAL300025051721 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051721

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051721/0 /scratch/stefan/7786831/working/building/REAL300025051721 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 601)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/601
`/scratch/stefan/7786831/working/3D/601' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC=CCCC2)CC1)

`REAL300025051721.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051721.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051721/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051721 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC=CCCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 72, 85, 160, 160, 160, 160, 160, 6, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 1, 1, 72, 72, 160, 23, 6, 6, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 46, 47, 48, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 434
number of broken/clashed sets: 201
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051721 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC=CCCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 33, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 133, 160, 160, 160, 160, 201, 201, 201, 201, 201, 201, 201, 160, 160, 33, 33, 1, 75, 133, 133, 160, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 160, 160, 160, 160] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 747
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051721 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC=CCCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 141, 157, 201, 201, 201, 201, 201, 22, 13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 141, 141, 201, 65, 22, 22, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13] 201
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 46, 47, 48, 49])
total number of confs: 660
number of broken/clashed sets: 201
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051721 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051721
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051721/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051721
Building REAL300025051722
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051722'
/scratch/stefan/7786831/working/building/REAL300025051722 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051722

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051722/0 /scratch/stefan/7786831/working/building/REAL300025051722 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 602)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/602
`/scratch/stefan/7786831/working/3D/602' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=NC=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051722.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051722.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051722/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051722 none COC1=CC=NC=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [11, 10, 10, 10, 10, 10, 10, 9, 2, 2, 2, 1, 1, 1, 4, 6, 6, 6, 18, 26, 50, 50, 50, 50, 50, 1, 1, 11, 11, 11, 10, 10, 10, 9, 9, 2, 4, 4, 6, 18, 18, 50, 1, 1, 1, 1] 62
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 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: REAL300025051722 none COC1=CC=NC=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 10, 10, 10, 10, 13, 15, 15, 15, 30, 38, 62, 62, 62, 62, 62, 10, 10, 3, 3, 3, 1, 1, 1, 3, 3, 10, 13, 13, 15, 30, 30, 62, 10, 10, 10, 10] 62
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 194
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051722 none COC1=CC=NC=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 50, 50, 50, 50, 47, 39, 39, 21, 39, 11, 1, 1, 1, 1, 1, 1, 1, 50, 50, 62, 62, 62, 62, 62, 62, 62, 62, 50, 47, 47, 39, 21, 21, 1, 50, 50, 50, 50] 62
rigid atoms, others: [41, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 242
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051722 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051722
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051722/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051722
Building REAL300025051723
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051723'
/scratch/stefan/7786831/working/building/REAL300025051723 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051723

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051723/0 /scratch/stefan/7786831/working/building/REAL300025051723 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 603)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/603
`/scratch/stefan/7786831/working/3D/603' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1C1CC1)

`REAL300025051723.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051723.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051723/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051723 none CC1C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 2, 2, 2, 1, 1, 1, 7, 23, 23, 23, 76, 103, 191, 191, 191, 191, 191, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 23, 76, 76, 191, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3] 201
rigid atoms, others: [37, 6, 7, 40, 39, 19, 20, 38, 5] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46])
total number of confs: 486
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051723 none CC1C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 3, 11, 35, 35, 35, 95, 122, 201, 201, 201, 201, 201, 3, 3, 1, 1, 2, 2, 1, 1, 1, 1, 1, 3, 11, 11, 35, 95, 95, 201, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 41, 21, 22, 25, 26, 27, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46])
total number of confs: 562
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051723 none CC1C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 2, 3, 3, 3, 3, 11, 35, 35, 35, 95, 122, 201, 201, 201, 201, 201, 3, 3, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 11, 11, 35, 95, 95, 201, 3, 3, 3, 3, 2, 1, 1, 1, 1, 1] 201
rigid atoms, others: [42, 43, 44, 45, 46, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 560
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051723 none CC1C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 191, 191, 191, 191, 148, 71, 71, 29, 71, 13, 1, 1, 1, 1, 1, 1, 1, 191, 191, 201, 201, 201, 201, 201, 201, 201, 201, 201, 191, 148, 148, 71, 29, 29, 1, 191, 191, 191, 191, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [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, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 762
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051723 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051723
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051723/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051723
Building REAL300025051724
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051724'
/scratch/stefan/7786831/working/building/REAL300025051724 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051724

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051724/0 /scratch/stefan/7786831/working/building/REAL300025051724 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 604)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/604
`/scratch/stefan/7786831/working/3D/604' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3CCCC[N@@H+]32)CC1)

`REAL300025051724.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051724.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051724/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051724 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3CCCC[N@@H+]32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 6, 6, 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: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [8, 8, 8, 17, 19, 27, 27, 27, 27, 27, 4, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 17, 17, 27, 8, 4, 4, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1] 31
rigid atoms, others: [11, 12, 13, 49, 50, 51, 52, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
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: REAL300025051724 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3CCCC[N@@H+]32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 6, 6, 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: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [23, 16, 12, 1, 1, 1, 1, 1, 1, 1, 23, 23, 26, 27, 27, 27, 27, 31, 31, 31, 31, 31, 31, 31, 31, 31, 27, 27, 16, 16, 1, 23, 26, 26, 27, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 27, 27, 27, 27] 31
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 101
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051724 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3CCCC[N@@H+]32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 6, 6, 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: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [16, 16, 16, 28, 29, 31, 31, 31, 31, 31, 9, 6, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 28, 28, 31, 16, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 31
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 49, 50, 51, 52])
total number of confs: 122
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051724 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051724/1 /scratch/stefan/7786831/working/building/REAL300025051724 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 605)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/605
`/scratch/stefan/7786831/working/3D/605' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3CCCC[N@H+]32)CC1)

`REAL300025051724.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051724.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051724/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051724 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3CCCC[N@H+]32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 6, 6, 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: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [13, 13, 13, 26, 28, 36, 36, 36, 36, 36, 4, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 26, 26, 36, 13, 4, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1] 42
rigid atoms, others: [11, 12, 13, 49, 50, 51, 52, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 130
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051724 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3CCCC[N@H+]32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 6, 6, 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: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [33, 22, 13, 1, 1, 1, 1, 1, 1, 1, 33, 33, 35, 36, 36, 36, 36, 42, 42, 42, 42, 42, 42, 42, 42, 42, 36, 36, 22, 22, 1, 33, 35, 35, 36, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 36, 36, 36, 36] 42
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 138
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051724 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC3CCCC[N@H+]32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 6, 6, 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: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [21, 21, 21, 36, 38, 42, 42, 42, 42, 42, 9, 7, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 36, 36, 42, 21, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 42
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 49, 50, 51, 52])
total number of confs: 147
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051724 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051724
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051724/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051724/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051724
Building REAL300025051725
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051725'
/scratch/stefan/7786831/working/building/REAL300025051725 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051725

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051725/0 /scratch/stefan/7786831/working/building/REAL300025051725 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 606)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/606
`/scratch/stefan/7786831/working/3D/606' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=NC=C1)

`REAL300025051725.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051725.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051725/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051725 none CC(CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=NC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 179, 112, 112, 112, 112, 94, 52, 52, 25, 52, 13, 1, 1, 1, 1, 1, 1, 1, 112, 112, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 179, 179, 112, 94, 94, 52, 25, 25, 1, 112, 112, 112, 112, 201, 201, 201, 201] 201
rigid atoms, others: [39, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 913
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051725 none CC(CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=NC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 2, 2, 1, 1, 1, 4, 7, 7, 7, 24, 37, 112, 112, 112, 112, 112, 1, 1, 21, 23, 23, 21, 23, 23, 21, 21, 21, 21, 9, 9, 2, 4, 4, 7, 24, 24, 112, 1, 1, 1, 1, 23, 23, 23, 23] 201
rigid atoms, others: [5, 6, 7, 40, 41, 42, 43, 19, 20] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47])
total number of confs: 320
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051725 none CC(CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=NC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 23, 23, 23, 23, 39, 59, 59, 59, 100, 126, 201, 201, 201, 201, 201, 23, 23, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 6, 23, 39, 39, 59, 100, 100, 201, 23, 23, 23, 23, 1, 1, 1, 1] 201
rigid atoms, others: [1, 44, 45, 46, 47, 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, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 616
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051725 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051725
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051725/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051725
Building REAL300025051726
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051726'
/scratch/stefan/7786831/working/building/REAL300025051726 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051726

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051726/0 /scratch/stefan/7786831/working/building/REAL300025051726 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 607)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/607
`/scratch/stefan/7786831/working/3D/607' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCC23CC3)CC1)

`REAL300025051726.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051726.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051726/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051726 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCC23CC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 27, 95, 112, 177, 177, 177, 177, 177, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 1, 1, 95, 95, 177, 27, 6, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [11, 44, 43, 12, 13, 46, 45, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 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: REAL300025051726 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCC23CC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [78, 33, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 150, 177, 177, 177, 177, 201, 201, 201, 201, 201, 201, 177, 177, 33, 33, 1, 78, 150, 150, 177, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 177, 177, 177, 177] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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, 45, 46])
total number of confs: 765
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051726 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCC23CC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [50, 50, 50, 139, 150, 201, 201, 201, 201, 201, 15, 7, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 139, 139, 201, 50, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 43, 44, 45, 46])
total number of confs: 636
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051726 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051726
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051726/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051726
Building REAL300025051727
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051727'
/scratch/stefan/7786831/working/building/REAL300025051727 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051727

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051727/0 /scratch/stefan/7786831/working/building/REAL300025051727 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 608)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/608
`/scratch/stefan/7786831/working/3D/608' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(COCC1CCCO1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051727.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051727.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051727/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051727 none O=C(COCC1CCCO1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 12, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 4, 11, 17, 21, 21, 21, 21, 1, 1, 1, 6, 17, 17, 17, 43, 59, 115, 115, 115, 115, 115, 1, 1, 4, 4, 17, 17, 21, 21, 21, 21, 21, 21, 21, 2, 6, 6, 17, 43, 43, 115, 1, 1, 1, 1] 201
rigid atoms, others: [44, 10, 11, 12, 45, 46, 47, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 358
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051727 none O=C(COCC1CCCO1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 12, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 14, 9, 4, 1, 1, 1, 1, 1, 1, 21, 21, 21, 37, 55, 55, 55, 111, 140, 201, 201, 201, 201, 201, 21, 21, 14, 14, 4, 4, 1, 1, 1, 1, 1, 1, 1, 21, 37, 37, 55, 111, 111, 201, 21, 21, 21, 21] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 36, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 646
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051727 none O=C(COCC1CCCO1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 12, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [115, 115, 115, 150, 188, 193, 201, 201, 201, 201, 115, 102, 79, 79, 54, 79, 13, 1, 1, 1, 1, 1, 1, 1, 115, 115, 150, 150, 193, 193, 201, 201, 201, 201, 201, 201, 201, 115, 102, 102, 79, 54, 54, 1, 115, 115, 115, 115] 201
rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47])
total number of confs: 757
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051727 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051727
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051727/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051727
Building REAL300025051728
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051728'
/scratch/stefan/7786831/working/building/REAL300025051728 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051728

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051728/0 /scratch/stefan/7786831/working/building/REAL300025051728 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 609)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/609
`/scratch/stefan/7786831/working/3D/609' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(NC(=O)C1CCC1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051728.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051728.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051728/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051728 none CC(NC(=O)C1CCC1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 2, 6, 8, 8, 8, 34, 34, 34, 2, 2, 1, 1, 1, 4, 6, 6, 6, 15, 20, 49, 49, 49, 49, 49, 1, 1, 6, 6, 6, 6, 8, 34, 34, 34, 34, 34, 34, 34, 2, 4, 4, 6, 15, 15, 49, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 46, 47, 48, 49, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 210
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051728 none CC(NC(=O)C1CCC1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 9, 9, 1, 9, 1, 1, 1, 1, 16, 34, 34, 34, 34, 51, 68, 68, 68, 115, 125, 201, 201, 201, 201, 201, 34, 34, 16, 16, 16, 16, 9, 1, 1, 1, 1, 1, 1, 1, 34, 51, 51, 68, 115, 115, 201, 34, 34, 34, 34] 201
rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 35, 38, 37] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 673
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051728 none CC(NC(=O)C1CCC1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [90, 49, 90, 90, 90, 90, 201, 201, 201, 49, 49, 49, 38, 28, 28, 17, 28, 11, 1, 1, 1, 1, 1, 1, 1, 49, 49, 90, 90, 90, 90, 90, 201, 201, 201, 201, 201, 201, 201, 49, 38, 38, 28, 17, 17, 1, 49, 49, 49, 49] 201
rigid atoms, others: [45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49])
total number of confs: 719
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051728 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051728
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051728/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051728
Building REAL300025051729
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051729'
/scratch/stefan/7786831/working/building/REAL300025051729 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051729

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051729/0 /scratch/stefan/7786831/working/building/REAL300025051729 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 610)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/610
`/scratch/stefan/7786831/working/3D/610' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NN1C)

`REAL300025051729.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051729.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051729/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051729 none CCC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 2, 2, 2, 2, 2, 2, 1, 1, 1, 7, 23, 23, 23, 61, 64, 108, 108, 108, 108, 108, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 7, 7, 23, 61, 61, 108, 1, 1, 1, 1, 2, 2, 2] 201
rigid atoms, others: [39, 8, 9, 42, 7, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 43, 44, 45])
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: REAL300025051729 none CCC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 23, 23, 23, 61, 64, 108, 108, 108, 108, 108, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 1, 2, 7, 7, 23, 61, 61, 108, 2, 2, 2, 2, 2, 2, 2] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 23, 24, 25, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 331
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051729 none CCC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 108, 108, 108, 108, 108, 108, 108, 70, 37, 37, 24, 37, 12, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 108, 108, 201, 201, 201, 201, 201, 108, 108, 70, 70, 37, 24, 24, 1, 108, 108, 108, 108, 108, 108, 108] 201
rigid atoms, others: [38, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 954
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051729 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051729
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051729/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051729
Building REAL300025051730
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051730'
/scratch/stefan/7786831/working/building/REAL300025051730 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051730

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051730/0 /scratch/stefan/7786831/working/building/REAL300025051730 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 611)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/611
`/scratch/stefan/7786831/working/3D/611' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CN=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1)

`REAL300025051730.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051730.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051730/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051730 none CCOC1=CN=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 7, 20, 20, 20, 81, 114, 198, 198, 198, 198, 198, 1, 1, 3, 3, 9, 9, 9, 9, 9, 3, 2, 7, 7, 20, 81, 81, 198, 1, 1, 1, 1, 3] 201
rigid atoms, others: [43, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44])
total number of confs: 524
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051730 none CCOC1=CN=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 9, 23, 23, 23, 85, 118, 199, 199, 199, 199, 199, 3, 3, 1, 1, 7, 7, 7, 6, 6, 1, 3, 9, 9, 23, 85, 85, 199, 3, 3, 3, 3, 1] 201
rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 44, 25, 26] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 540
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051730 none CCOC1=CN=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 199, 199, 199, 199, 198, 198, 198, 198, 138, 74, 74, 30, 74, 13, 1, 1, 1, 1, 1, 1, 1, 198, 198, 199, 199, 201, 201, 201, 201, 201, 199, 198, 138, 138, 74, 30, 30, 1, 198, 198, 198, 198, 199] 201
rigid atoms, others: [39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44])
total number of confs: 753
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051730 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051730
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051730/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051730
Building REAL300025051731
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051731'
/scratch/stefan/7786831/working/building/REAL300025051731 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051731

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051731/0 /scratch/stefan/7786831/working/building/REAL300025051731 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 612)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/612
`/scratch/stefan/7786831/working/3D/612' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1N=C(C)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1)

`REAL300025051731.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051731.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051731/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051731 none CCN1N=C(C)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 15, 15, 15, 48, 55, 117, 117, 117, 117, 117, 1, 1, 4, 7, 7, 7, 7, 7, 4, 4, 4, 2, 7, 7, 15, 48, 48, 117, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
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: REAL300025051731 none CCN1N=C(C)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 3, 3, 4, 4, 11, 20, 20, 20, 56, 62, 117, 117, 117, 117, 117, 4, 4, 1, 3, 3, 3, 3, 3, 2, 2, 2, 4, 11, 11, 20, 56, 56, 117, 4, 4, 4, 4] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 25] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 341
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051731 none CCN1N=C(C)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 117, 117, 117, 117, 117, 117, 117, 117, 117, 77, 45, 45, 27, 45, 12, 1, 1, 1, 1, 1, 1, 1, 117, 117, 117, 201, 201, 201, 201, 201, 117, 117, 117, 117, 77, 77, 45, 27, 27, 1, 117, 117, 117, 117] 201
rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 948
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051731 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051731
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051731/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051731
Building REAL300025051732
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051732'
/scratch/stefan/7786831/working/building/REAL300025051732 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051732

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051732/0 /scratch/stefan/7786831/working/building/REAL300025051732 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 613)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/613
`/scratch/stefan/7786831/working/3D/613' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CN=CC(F)=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051732.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051732.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051732/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051732 none O=C(CCC1=CN=CC(F)=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 5, 1, 1, 8, 1, 1, 15, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 10, 12, 21, 21, 21, 21, 21, 21, 1, 1, 1, 6, 12, 12, 12, 32, 46, 99, 99, 99, 99, 99, 1, 1, 10, 10, 12, 12, 21, 21, 21, 2, 6, 6, 12, 32, 32, 99, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 42, 11, 12, 13, 44, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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])
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: REAL300025051732 none O=C(CCC1=CN=CC(F)=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 5, 1, 1, 8, 1, 1, 15, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 20, 21, 21, 44, 59, 59, 59, 100, 125, 201, 201, 201, 201, 201, 21, 21, 5, 5, 2, 2, 1, 1, 1, 21, 44, 44, 59, 100, 100, 201, 21, 21, 21, 21] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 640
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051732 none O=C(CCC1=CN=CC(F)=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 5, 1, 1, 8, 1, 1, 15, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [99, 99, 99, 152, 154, 201, 201, 201, 201, 201, 201, 99, 87, 50, 50, 26, 50, 13, 1, 1, 1, 1, 1, 1, 1, 99, 99, 152, 152, 154, 154, 201, 201, 201, 99, 87, 87, 50, 26, 26, 1, 99, 99, 99, 99] 201
rigid atoms, others: [40, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 737
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051732 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051732
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051732/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051732
Building REAL300025051733
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051733'
/scratch/stefan/7786831/working/building/REAL300025051733 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051733

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051733/0 /scratch/stefan/7786831/working/building/REAL300025051733 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 614)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/614
`/scratch/stefan/7786831/working/3D/614' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=N1)

`REAL300025051733.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051733.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051733/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051733 none CN1C=C(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 13, 9, 2, 2, 2, 1, 1, 1, 6, 14, 14, 14, 57, 89, 184, 184, 184, 184, 184, 1, 1, 21, 21, 21, 21, 21, 21, 13, 13, 9, 9, 2, 6, 6, 14, 57, 57, 184, 1, 1, 1, 1] 201
rigid atoms, others: [43, 8, 9, 10, 23, 44, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
total number of confs: 478
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051733 none CN1C=C(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 6, 13, 21, 21, 21, 21, 28, 41, 41, 41, 92, 129, 201, 201, 201, 201, 201, 21, 21, 1, 1, 2, 2, 2, 1, 6, 6, 13, 13, 21, 28, 28, 41, 92, 92, 201, 21, 21, 21, 21] 201
rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 599
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051733 none CN1C=C(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 200, 184, 184, 184, 184, 147, 90, 90, 33, 90, 13, 1, 1, 1, 1, 1, 1, 1, 184, 184, 201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 184, 147, 147, 90, 33, 33, 1, 184, 184, 184, 184] 201
rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 779
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051733 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051733
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051733/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051733
Building REAL300025051734
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051734'
/scratch/stefan/7786831/working/building/REAL300025051734 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051734

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051734/0 /scratch/stefan/7786831/working/building/REAL300025051734 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 615)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/615
`/scratch/stefan/7786831/working/3D/615' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC1=NC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1)

`REAL300025051734.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051734.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051734/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051734 none COCC1=NC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 9, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 4, 8, 8, 8, 26, 43, 129, 129, 129, 129, 129, 1, 1, 3, 12, 12, 12, 9, 9, 3, 2, 4, 4, 8, 26, 26, 129, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 287
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051734 none COCC1=NC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 10, 10, 10, 29, 48, 133, 133, 133, 133, 133, 3, 3, 1, 9, 9, 9, 5, 5, 1, 3, 5, 5, 10, 29, 29, 133, 3, 3, 3, 3] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 25, 31] set([0, 1, 8, 9, 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])
total number of confs: 291
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051734 none COCC1=NC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 133, 133, 133, 133, 129, 129, 129, 129, 108, 58, 58, 27, 58, 13, 1, 1, 1, 1, 1, 1, 1, 129, 129, 133, 201, 201, 201, 201, 201, 133, 129, 108, 108, 58, 27, 27, 1, 129, 129, 129, 129] 201
rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 904
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051734 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051734
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051734/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051734
Building REAL300025051735
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051735'
/scratch/stefan/7786831/working/building/REAL300025051735 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051735

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051735/0 /scratch/stefan/7786831/working/building/REAL300025051735 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 616)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/616
`/scratch/stefan/7786831/working/3D/616' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1)

`REAL300025051735.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051735.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051735/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051735 none CC1=CC=C(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 16, 10, 2, 2, 2, 1, 1, 1, 4, 7, 7, 7, 23, 37, 98, 98, 98, 98, 98, 1, 1, 28, 28, 28, 28, 28, 28, 16, 16, 10, 10, 2, 4, 4, 7, 23, 23, 98, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
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: REAL300025051735 none CC1=CC=C(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 4, 8, 27, 27, 28, 28, 43, 64, 64, 64, 114, 140, 201, 201, 201, 201, 201, 28, 28, 1, 2, 2, 2, 1, 1, 4, 4, 8, 8, 28, 43, 43, 64, 114, 114, 201, 28, 28, 28, 28] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 681
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051735 none CC1=CC=C(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 193, 180, 98, 98, 98, 98, 80, 47, 47, 23, 47, 12, 1, 1, 1, 1, 1, 1, 1, 98, 98, 201, 201, 201, 201, 201, 201, 193, 193, 180, 180, 98, 80, 80, 47, 23, 23, 1, 98, 98, 98, 98] 201
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 840
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051735 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051735
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051735/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051735
Building REAL300025051736
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051736'
/scratch/stefan/7786831/working/building/REAL300025051736 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051736

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051736/0 /scratch/stefan/7786831/working/building/REAL300025051736 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 617)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/617
`/scratch/stefan/7786831/working/3D/617' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1CCC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1)

`REAL300025051736.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051736.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051736/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051736 none COC1CCC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 17, 17, 17, 17, 8, 2, 2, 2, 1, 1, 1, 4, 10, 10, 10, 37, 54, 108, 108, 108, 108, 108, 1, 1, 17, 17, 25, 25, 25, 17, 17, 17, 17, 17, 17, 8, 8, 2, 4, 4, 10, 37, 37, 108, 1, 1, 1, 1, 17, 17, 17, 17] 201
rigid atoms, others: [9, 10, 11, 45, 46, 47, 48, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52])
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: REAL300025051736 none COC1CCC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 17, 17, 17, 17, 30, 49, 49, 49, 102, 139, 201, 201, 201, 201, 201, 17, 17, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 17, 30, 30, 49, 102, 102, 201, 17, 17, 17, 17, 1, 1, 1, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 34, 49, 50, 35, 52, 25, 26, 51, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 620
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051736 none COC1CCC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 184, 108, 108, 108, 108, 92, 66, 66, 46, 66, 13, 1, 1, 1, 1, 1, 1, 1, 108, 108, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 184, 184, 108, 92, 92, 66, 46, 46, 1, 108, 108, 108, 108, 201, 201, 201, 201] 201
rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 863
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051736 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051736
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051736/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051736
Building REAL300025051737
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051737'
/scratch/stefan/7786831/working/building/REAL300025051737 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051737

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051737/0 /scratch/stefan/7786831/working/building/REAL300025051737 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 618)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/618
`/scratch/stefan/7786831/working/3D/618' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CCCCC1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051737.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051737.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051737/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051737 none CC1(C)CCCCC1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 9, 2, 2, 2, 1, 1, 1, 7, 15, 15, 15, 45, 62, 143, 143, 143, 143, 143, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 2, 7, 7, 15, 45, 45, 143, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 51, 52, 53, 54, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 374
number of broken/clashed sets: 56
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051737 none CC1(C)CCCCC1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 3, 13, 13, 13, 13, 28, 39, 39, 39, 96, 118, 201, 201, 201, 201, 201, 13, 13, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 28, 28, 39, 96, 96, 201, 13, 13, 13, 13] 201
rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 40, 41, 36, 34, 8, 35, 39, 4, 38, 5, 37, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 589
number of broken/clashed sets: 56
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051737 none CC1(C)CCCCC1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 143, 143, 143, 143, 98, 56, 56, 27, 56, 13, 1, 1, 1, 1, 1, 1, 1, 143, 143, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 143, 98, 98, 56, 27, 27, 1, 143, 143, 143, 143] 201
rigid atoms, others: [50, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54])
total number of confs: 841
number of broken/clashed sets: 56
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051737 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051737
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051737/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051737
Building REAL300025051738
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051738'
/scratch/stefan/7786831/working/building/REAL300025051738 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051738

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051738/0 /scratch/stefan/7786831/working/building/REAL300025051738 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 619)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/619
`/scratch/stefan/7786831/working/3D/619' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)NC=N1)

`REAL300025051738.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051738.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051738/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051738 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 2, 2, 2, 1, 1, 1, 5, 18, 18, 18, 34, 39, 59, 59, 59, 59, 59, 1, 1, 8, 8, 8, 8, 8, 8, 2, 5, 5, 18, 34, 34, 59, 1, 1, 1, 1, 8, 8] 67
rigid atoms, others: [34, 35, 36, 5, 6, 7, 19, 20, 37] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39])
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: REAL300025051738 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
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, 8, 8, 8, 8, 16, 35, 35, 35, 54, 57, 67, 67, 67, 67, 67, 8, 8, 1, 1, 1, 2, 2, 2, 8, 16, 16, 35, 54, 54, 67, 8, 8, 8, 8, 1, 1] 67
rigid atoms, others: [0, 1, 2, 3, 38, 39, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 234
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051738 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 59, 59, 59, 59, 54, 42, 42, 24, 42, 11, 1, 1, 1, 1, 1, 1, 1, 59, 59, 67, 67, 67, 67, 67, 67, 59, 54, 54, 42, 24, 24, 1, 59, 59, 59, 59, 67, 67] 67
rigid atoms, others: [33, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39])
total number of confs: 229
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051738 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051738
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051738/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051738
Building REAL300025051739
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051739'
/scratch/stefan/7786831/working/building/REAL300025051739 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051739

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051739/0 /scratch/stefan/7786831/working/building/REAL300025051739 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 620)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/620
`/scratch/stefan/7786831/working/3D/620' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)N1CCOCC1)

`REAL300025051739.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051739.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051739/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051739 none C[C@@H](C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)N1CCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 188, 201, 188, 188, 188, 137, 63, 63, 30, 63, 13, 1, 1, 1, 1, 1, 1, 1, 188, 188, 201, 201, 201, 201, 201, 201, 201, 201, 201, 188, 137, 137, 63, 30, 30, 1, 188, 188, 188, 188, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [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, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 774
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051739 none C[C@@H](C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)N1CCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 6, 2, 2, 1, 1, 1, 7, 23, 23, 23, 76, 102, 188, 188, 188, 188, 188, 1, 1, 6, 7, 7, 7, 7, 7, 6, 6, 6, 2, 7, 7, 23, 76, 76, 188, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] 201
rigid atoms, others: [37, 6, 7, 40, 39, 19, 20, 38, 5] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 492
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051739 none C[C@@H](C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)N1CCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 7, 7, 7, 7, 17, 36, 36, 36, 97, 122, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 6, 6, 6, 7, 17, 17, 36, 97, 97, 201, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 48, 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, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 579
number of broken/clashed sets: 30
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051739 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051739
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051739/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051739
Building REAL300025051740
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051740'
/scratch/stefan/7786831/working/building/REAL300025051740 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051740

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051740/0 /scratch/stefan/7786831/working/building/REAL300025051740 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 621)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/621
`/scratch/stefan/7786831/working/3D/621' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC23CCOCC3)CC1)

`REAL300025051740.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051740.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051740/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051740 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC23CCOCC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 71, 83, 163, 163, 163, 163, 163, 6, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 1, 1, 71, 71, 163, 22, 6, 6, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1] 201
rigid atoms, others: [44, 11, 12, 13, 46, 45, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 428
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051740 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC23CCOCC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 31, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 121, 163, 163, 163, 163, 201, 201, 201, 201, 201, 201, 201, 163, 163, 31, 31, 1, 61, 121, 121, 163, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 163, 163, 163, 163] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 757
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051740 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC23CCOCC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [55, 55, 55, 134, 146, 201, 201, 201, 201, 201, 14, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 134, 134, 201, 55, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 44, 45, 46, 47])
total number of confs: 646
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051740 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051740
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051740/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051740
Building REAL300025051741
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051741'
/scratch/stefan/7786831/working/building/REAL300025051741 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051741

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051741/0 /scratch/stefan/7786831/working/building/REAL300025051741 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 622)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/622
`/scratch/stefan/7786831/working/3D/622' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CCC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1)

`REAL300025051741.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051741.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051741/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051741 none CC1(C)CCC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 24, 23, 10, 2, 2, 2, 1, 1, 1, 4, 13, 13, 13, 24, 37, 84, 84, 84, 84, 84, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 2, 4, 4, 13, 24, 24, 84, 1, 1, 1, 1, 24, 24, 24, 24] 201
rigid atoms, others: [9, 10, 11, 47, 48, 49, 50, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52, 53, 54])
total number of confs: 266
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051741 none CC1(C)CCC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 24, 24, 24, 24, 42, 85, 85, 85, 115, 150, 201, 201, 201, 201, 201, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 42, 42, 85, 115, 115, 201, 24, 24, 24, 24, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 51, 52, 53, 54] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 621
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051741 none CC1(C)CCC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 185, 84, 84, 84, 84, 70, 53, 53, 38, 53, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 185, 185, 84, 70, 70, 53, 38, 38, 1, 84, 84, 84, 84, 201, 201, 201, 201] 201
rigid atoms, others: [46, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 839
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051741 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051741
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051741/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051741
Building REAL300025051742
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051742'
/scratch/stefan/7786831/working/building/REAL300025051742 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051742

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051742/0 /scratch/stefan/7786831/working/building/REAL300025051742 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 623)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/623
`/scratch/stefan/7786831/working/3D/623' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCOCC1)

`REAL300025051742.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051742.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051742/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051742 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 152, 152, 152, 114, 53, 53, 28, 53, 13, 1, 1, 1, 1, 1, 1, 1, 152, 152, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 152, 114, 114, 53, 28, 28, 1, 152, 152, 152, 152, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [36, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 839
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051742 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 2, 1, 1, 1, 7, 18, 18, 18, 51, 65, 152, 152, 152, 152, 152, 1, 1, 5, 6, 6, 6, 6, 6, 5, 5, 5, 5, 2, 7, 7, 18, 51, 51, 152, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6] 201
rigid atoms, others: [4, 5, 6, 39, 40, 18, 19, 38, 37] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 375
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051742 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 6, 6, 18, 36, 36, 36, 89, 108, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 6, 18, 18, 36, 89, 89, 201, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 48, 49, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 558
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051742 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051742
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051742/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051742
Building REAL300025051743
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051743'
/scratch/stefan/7786831/working/building/REAL300025051743 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051743

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051743/0 /scratch/stefan/7786831/working/building/REAL300025051743 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 624)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/624
`/scratch/stefan/7786831/working/3D/624' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CC(=O)NC2=O)CC1)

`REAL300025051743.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051743.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051743/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051743 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CC(=O)NC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 28, 37, 100, 100, 100, 100, 100, 5, 1, 1, 1, 3, 3, 3, 19, 40, 40, 40, 40, 40, 40, 1, 1, 28, 28, 100, 12, 5, 5, 3, 19, 19, 40, 40, 40, 40, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 336
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051743 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CC(=O)NC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 30, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 94, 100, 100, 100, 100, 189, 201, 201, 201, 201, 201, 201, 100, 100, 30, 30, 1, 66, 94, 94, 100, 189, 189, 201, 201, 201, 201, 100, 100, 100, 100] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 814
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051743 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CC(=O)NC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [94, 94, 94, 133, 145, 201, 201, 201, 201, 201, 49, 40, 29, 29, 7, 29, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 133, 133, 201, 94, 49, 49, 29, 7, 7, 1, 1, 1, 1, 40, 40, 40, 40] 201
rigid atoms, others: [35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42])
total number of confs: 651
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051743 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051743
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051743/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051743
Building REAL300025051744
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051744'
/scratch/stefan/7786831/working/building/REAL300025051744 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051744

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051744/0 /scratch/stefan/7786831/working/building/REAL300025051744 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 625)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/625
`/scratch/stefan/7786831/working/3D/625' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NN1C(C)C)

`REAL300025051744.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051744.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051744/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051744 none CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NN1C(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 5, 5, 5, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 26, 26, 26, 83, 96, 187, 187, 187, 187, 187, 1, 1, 4, 4, 4, 8, 8, 4, 4, 4, 4, 2, 7, 7, 26, 83, 83, 187, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8] 201
rigid atoms, others: [6, 38, 7, 8, 41, 39, 40, 20, 21] set([0, 1, 2, 3, 4, 5, 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, 36, 37, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 512
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051744 none CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NN1C(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 5, 5, 5, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 4, 4, 13, 35, 35, 35, 102, 117, 200, 201, 201, 201, 201, 4, 4, 1, 1, 1, 3, 3, 2, 2, 2, 1, 4, 13, 13, 35, 102, 102, 201, 4, 4, 4, 4, 3, 4, 4, 4, 3, 3, 3] 201
rigid atoms, others: [0, 1, 2, 3, 4, 22, 23, 24, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 599
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051744 none CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NN1C(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 5, 5, 5, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 187, 187, 187, 124, 48, 48, 27, 48, 13, 1, 1, 1, 1, 1, 1, 1, 187, 187, 201, 201, 201, 201, 201, 201, 201, 201, 201, 187, 124, 124, 48, 27, 27, 1, 187, 187, 187, 187, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [37, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 718
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051744 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051744
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051744/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051744
Building REAL300025051745
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051745'
/scratch/stefan/7786831/working/building/REAL300025051745 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051745

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051745/0 /scratch/stefan/7786831/working/building/REAL300025051745 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 626)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/626
`/scratch/stefan/7786831/working/3D/626' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCC(=O)N1)

`REAL300025051745.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051745.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051745/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051745 none CC1(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 9, 9, 2, 2, 2, 1, 1, 1, 4, 9, 9, 9, 27, 43, 120, 120, 120, 120, 120, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 9, 9, 9, 9, 2, 4, 4, 9, 27, 27, 120, 1, 1, 1, 1, 15, 15, 15, 15, 15] 201
rigid atoms, others: [6, 7, 8, 41, 42, 43, 44, 20, 21] set([0, 1, 2, 3, 4, 5, 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, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49])
total number of confs: 287
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051745 none CC1(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 3, 15, 15, 15, 15, 32, 50, 50, 50, 105, 137, 201, 201, 201, 201, 201, 15, 15, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 15, 32, 32, 50, 105, 105, 201, 15, 15, 15, 15, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 45, 46, 47, 48, 49, 22, 23, 24, 25, 26] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 638
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051745 none CC1(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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, 120, 120, 120, 120, 97, 56, 56, 28, 56, 13, 1, 1, 1, 1, 1, 1, 1, 120, 120, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 120, 97, 97, 56, 28, 28, 1, 120, 120, 120, 120, 201, 201, 201, 201, 201] 201
rigid atoms, others: [40, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 885
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051745 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051745
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051745/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051745
Building REAL300025051746
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051746'
/scratch/stefan/7786831/working/building/REAL300025051746 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051746

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051746/0 /scratch/stefan/7786831/working/building/REAL300025051746 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 627)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/627
`/scratch/stefan/7786831/working/3D/627' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN3CCCCC3=C2)CC1)

`REAL300025051746.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051746.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051746/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051746 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN3CCCCC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 58, 66, 100, 100, 100, 100, 100, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 58, 58, 100, 18, 5, 5, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1] 201
rigid atoms, others: [44, 11, 12, 13, 46, 45, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
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: REAL300025051746 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN3CCCCC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [54, 28, 13, 1, 1, 1, 1, 1, 1, 1, 54, 54, 86, 100, 100, 100, 100, 201, 201, 201, 201, 201, 201, 201, 201, 100, 100, 28, 28, 1, 54, 86, 86, 100, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 100, 100, 100, 100] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46, 47])
total number of confs: 532
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051746 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN3CCCCC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 155, 165, 201, 201, 201, 201, 201, 17, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 155, 155, 201, 62, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 44, 45, 46, 47])
total number of confs: 693
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051746 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051746
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051746/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051746
Building REAL300025051747
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051747'
/scratch/stefan/7786831/working/building/REAL300025051747 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051747

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051747/0 /scratch/stefan/7786831/working/building/REAL300025051747 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 628)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/628
`/scratch/stefan/7786831/working/3D/628' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C1=CC=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051747.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051747.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051747/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051747 none NC(=O)C1=CC=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 4, 5, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 29, 29, 29, 83, 96, 189, 190, 190, 190, 190, 1, 1, 4, 5, 5, 4, 4, 2, 7, 7, 29, 83, 83, 190, 1, 1, 1, 1, 4] 201
rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42])
total number of confs: 490
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051747 none NC(=O)C1=CC=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 13, 44, 44, 44, 107, 120, 190, 190, 190, 190, 190, 4, 4, 1, 3, 3, 1, 1, 4, 13, 13, 44, 107, 107, 190, 4, 4, 4, 4, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 42, 26, 29, 30] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 560
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051747 none NC(=O)C1=CC=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 190, 201, 190, 190, 190, 190, 190, 190, 190, 190, 120, 52, 52, 27, 52, 13, 1, 1, 1, 1, 1, 1, 1, 190, 190, 190, 201, 201, 190, 190, 190, 120, 120, 52, 27, 27, 1, 190, 190, 190, 190, 190] 201
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 729
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051747 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051747
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051747/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051747
Building REAL300025051748
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051748'
/scratch/stefan/7786831/working/building/REAL300025051748 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051748

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051748/0 /scratch/stefan/7786831/working/building/REAL300025051748 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 629)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/629
`/scratch/stefan/7786831/working/3D/629' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C1=NC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1)

`REAL300025051748.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051748.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051748/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051748 none CC(C)C1=NC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 5, 14, 5, 5, 5, 2, 2, 2, 1, 1, 1, 6, 15, 15, 15, 50, 92, 191, 191, 191, 191, 191, 1, 1, 5, 14, 14, 14, 14, 14, 14, 14, 5, 2, 6, 6, 15, 50, 50, 191, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 454
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051748 none CC(C)C1=NC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 1, 5, 5, 5, 5, 10, 20, 20, 20, 58, 100, 197, 197, 197, 197, 197, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 1, 5, 10, 10, 20, 58, 58, 197, 5, 5, 5, 5] 201
rigid atoms, others: [1, 3, 4, 5, 6, 33, 7, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 461
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051748 none CC(C)C1=NC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 197, 201, 197, 197, 197, 191, 191, 191, 191, 156, 82, 82, 29, 82, 13, 1, 1, 1, 1, 1, 1, 1, 191, 191, 197, 201, 201, 201, 201, 201, 201, 201, 197, 191, 156, 156, 82, 29, 29, 1, 191, 191, 191, 191] 201
rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 750
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051748 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051748
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051748/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051748
Building REAL300025051749
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051749'
/scratch/stefan/7786831/working/building/REAL300025051749 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051749

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051749/0 /scratch/stefan/7786831/working/building/REAL300025051749 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 630)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/630
`/scratch/stefan/7786831/working/3D/630' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CC)C(=O)NCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051749.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051749.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051749/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051749 none CCC(CC)C(=O)NCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [99, 92, 65, 92, 99, 65, 65, 64, 60, 60, 60, 60, 59, 51, 51, 40, 51, 12, 1, 1, 1, 1, 1, 1, 1, 60, 60, 99, 99, 99, 99, 99, 92, 99, 99, 99, 99, 99, 65, 64, 64, 60, 59, 59, 51, 40, 40, 1, 60, 60, 60, 60] 99
rigid atoms, others: [47, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51])
total number of confs: 449
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051749 none CCC(CC)C(=O)NCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [13, 9, 6, 9, 12, 6, 6, 5, 2, 2, 2, 1, 1, 1, 4, 7, 7, 7, 16, 28, 60, 60, 60, 60, 60, 1, 1, 13, 13, 13, 13, 13, 9, 12, 12, 12, 12, 12, 6, 5, 5, 2, 4, 4, 7, 16, 16, 60, 1, 1, 1, 1] 99
rigid atoms, others: [11, 12, 13, 48, 49, 50, 51, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 202
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051749 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051749
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051749/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051749
Building REAL300025051750
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051750'
/scratch/stefan/7786831/working/building/REAL300025051750 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051750

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051750/0 /scratch/stefan/7786831/working/building/REAL300025051750 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 631)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/631
`/scratch/stefan/7786831/working/3D/631' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCCCC1)

`REAL300025051750.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051750.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051750/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051750 none COC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [184, 184, 128, 128, 128, 128, 87, 46, 46, 26, 46, 13, 1, 1, 1, 1, 1, 1, 1, 128, 128, 184, 201, 201, 201, 201, 201, 184, 184, 184, 184, 128, 87, 87, 46, 26, 26, 1, 128, 128, 128, 128, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [37, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 878
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051750 none COC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 2, 2, 1, 1, 1, 7, 15, 15, 15, 47, 56, 128, 128, 128, 128, 128, 1, 1, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 2, 7, 7, 15, 47, 47, 128, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 201
rigid atoms, others: [5, 38, 7, 40, 41, 39, 19, 20, 6] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 332
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051750 none COC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1CCCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 4, 5, 5, 5, 5, 19, 40, 40, 40, 99, 113, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 5, 19, 19, 40, 99, 99, 201, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [2, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 594
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051750 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051750
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051750/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051750
Building REAL300025051751
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051751'
/scratch/stefan/7786831/working/building/REAL300025051751 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051751

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051751/0 /scratch/stefan/7786831/working/building/REAL300025051751 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 632)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/632
`/scratch/stefan/7786831/working/3D/632' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)O1)

`REAL300025051751.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051751.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051751/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051751 none CCC1=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 3, 3, 3, 2, 2, 2, 1, 1, 1, 7, 15, 15, 15, 49, 61, 125, 125, 125, 125, 125, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 2, 7, 7, 15, 49, 49, 125, 1, 1, 1, 1, 3, 3, 3] 201
rigid atoms, others: [38, 7, 8, 9, 39, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 42, 43, 44])
total number of confs: 354
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051751 none CCC1=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 1, 1, 1, 1, 2, 2, 3, 3, 8, 16, 16, 16, 51, 64, 127, 127, 127, 127, 127, 3, 3, 1, 1, 1, 8, 8, 8, 7, 7, 3, 8, 8, 16, 51, 51, 127, 3, 3, 3, 3, 2, 2, 2] 201
rigid atoms, others: [1, 2, 3, 4, 5, 23, 24, 25] set([0, 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, 41, 42, 43, 44])
total number of confs: 360
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051751 none CCC1=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 127, 127, 127, 125, 125, 125, 125, 82, 44, 44, 25, 44, 13, 1, 1, 1, 1, 1, 1, 1, 125, 125, 127, 127, 127, 201, 201, 201, 201, 201, 125, 82, 82, 44, 25, 25, 1, 125, 125, 125, 125, 127, 127, 127] 201
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 910
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051751 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051751
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051751/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051751
Building REAL300025051752
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051752'
/scratch/stefan/7786831/working/building/REAL300025051752 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051752

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051752/0 /scratch/stefan/7786831/working/building/REAL300025051752 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 633)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/633
`/scratch/stefan/7786831/working/3D/633' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C(C)C(C)(C)C)

`REAL300025051752.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051752.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051752/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051752 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C(C)C(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 200, 200, 200, 167, 83, 83, 29, 83, 13, 1, 1, 1, 1, 1, 1, 1, 200, 200, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 167, 167, 83, 29, 29, 1, 200, 200, 200, 200, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [36, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 766
number of broken/clashed sets: 201
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051752 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C(C)C(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 3, 1, 1, 1, 7, 22, 22, 22, 85, 126, 200, 200, 200, 200, 200, 1, 1, 4, 4, 4, 5, 5, 5, 4, 4, 4, 4, 3, 7, 7, 22, 85, 85, 200, 1, 1, 1, 1, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5] 201
rigid atoms, others: [4, 5, 6, 39, 40, 18, 19, 38, 37] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 524
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051752 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051752
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051752/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051752
Building REAL300025051753
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051753'
/scratch/stefan/7786831/working/building/REAL300025051753 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051753

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051753/0 /scratch/stefan/7786831/working/building/REAL300025051753 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 634)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/634
`/scratch/stefan/7786831/working/3D/634' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1=CC=CO1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051753.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051753.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051753/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051753 none CC(CC1=CC=CO1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 2, 6, 10, 16, 16, 16, 16, 2, 2, 1, 1, 1, 6, 15, 15, 15, 52, 77, 162, 162, 162, 162, 162, 1, 1, 6, 6, 6, 6, 10, 10, 16, 16, 16, 2, 6, 6, 15, 52, 52, 162, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 434
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051753 none CC(CC1=CC=CO1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 4, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 16, 25, 39, 39, 39, 86, 119, 201, 201, 201, 201, 201, 16, 16, 7, 7, 7, 7, 4, 4, 1, 1, 1, 16, 25, 25, 39, 86, 86, 201, 16, 16, 16, 16] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 570
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051753 none CC(CC1=CC=CO1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [184, 162, 184, 186, 201, 201, 201, 201, 162, 162, 162, 131, 72, 72, 28, 72, 13, 1, 1, 1, 1, 1, 1, 1, 162, 162, 184, 184, 184, 184, 186, 186, 201, 201, 201, 162, 131, 131, 72, 28, 28, 1, 162, 162, 162, 162] 201
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 762
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051753 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051753
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051753/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051753
Building REAL300025051754
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051754'
/scratch/stefan/7786831/working/building/REAL300025051754 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051754

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051754/0 /scratch/stefan/7786831/working/building/REAL300025051754 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 635)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/635
`/scratch/stefan/7786831/working/3D/635' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025051754.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051754.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051754/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051754 none CC1CCC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 22, 10, 2, 2, 2, 1, 1, 1, 4, 6, 6, 6, 19, 28, 89, 89, 89, 89, 89, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10, 10, 2, 4, 4, 6, 19, 19, 89, 1, 1, 1, 1, 22, 22] 201
rigid atoms, others: [8, 9, 10, 43, 44, 45, 46, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 47, 48])
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: REAL300025051754 none CC1CCC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 22, 22, 22, 22, 43, 58, 58, 58, 102, 133, 201, 201, 201, 201, 201, 22, 22, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 22, 43, 43, 58, 102, 102, 201, 22, 22, 22, 22, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 47, 48, 24, 33, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 660
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051754 none CC1CCC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 192, 89, 89, 89, 89, 80, 49, 49, 25, 49, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 192, 192, 89, 80, 80, 49, 25, 25, 1, 89, 89, 89, 89, 201, 201] 201
rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48])
total number of confs: 834
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051754 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051754
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051754/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051754
Building REAL300025051755
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051755'
/scratch/stefan/7786831/working/building/REAL300025051755 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051755

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051755/0 /scratch/stefan/7786831/working/building/REAL300025051755 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 636)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/636
`/scratch/stefan/7786831/working/3D/636' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N(C)N=C1)

`REAL300025051755.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051755.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051755/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051755 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N(C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 2, 2, 2, 1, 1, 1, 4, 20, 20, 20, 83, 97, 163, 163, 163, 163, 163, 1, 1, 8, 8, 8, 8, 8, 8, 8, 2, 4, 4, 20, 83, 83, 163, 1, 1, 1, 1, 8, 8, 8, 8] 201
rigid atoms, others: [35, 36, 5, 6, 7, 19, 20, 38, 37] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42])
total number of confs: 445
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: REAL300025051755 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N(C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 8, 8, 8, 8, 14, 45, 45, 45, 133, 148, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 2, 2, 2, 8, 14, 14, 45, 133, 133, 201, 8, 8, 8, 8, 2, 2, 2, 1] 201
rigid atoms, others: [0, 1, 2, 3, 42, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 635
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051755 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N(C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 163, 163, 163, 163, 129, 68, 68, 28, 68, 13, 1, 1, 1, 1, 1, 1, 1, 163, 163, 201, 201, 201, 201, 201, 201, 201, 163, 129, 129, 68, 28, 28, 1, 163, 163, 163, 163, 201, 201, 201, 201] 201
rigid atoms, others: [34, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 674
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051755 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051755
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051755/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051755
Building REAL300025051756
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051756'
/scratch/stefan/7786831/working/building/REAL300025051756 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051756

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051756/0 /scratch/stefan/7786831/working/building/REAL300025051756 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 637)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/637
`/scratch/stefan/7786831/working/3D/637' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(F)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051756.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051756.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051756/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051756 none CC(C)C(F)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
168  conformations in input
total number of sets (complete confs): 168
using faster count positions algorithm for large data
unique positions, atoms: [168, 153, 168, 77, 153, 77, 77, 77, 72, 55, 55, 25, 55, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 168, 168, 168, 168, 168, 168, 168, 153, 77, 72, 72, 55, 25, 25, 1, 77, 77, 77, 77] 168
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41])
total number of confs: 721
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051756 none CC(C)C(F)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
168  conformations in input
total number of sets (complete confs): 168
using faster count positions algorithm for large data
unique positions, atoms: [25, 11, 26, 2, 11, 2, 2, 1, 1, 1, 4, 16, 16, 16, 36, 41, 77, 77, 77, 77, 77, 1, 1, 26, 26, 26, 26, 26, 26, 26, 11, 2, 4, 4, 16, 36, 36, 77, 1, 1, 1, 1] 168
rigid atoms, others: [38, 7, 8, 9, 39, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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])
total number of confs: 313
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051756 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051756
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051756/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051756
Building REAL300025051757
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051757'
/scratch/stefan/7786831/working/building/REAL300025051757 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051757

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051757/0 /scratch/stefan/7786831/working/building/REAL300025051757 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 638)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/638
`/scratch/stefan/7786831/working/3D/638' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(C)C(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051757.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051757.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051757/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051757 none C=CC(C)C(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 193, 201, 143, 193, 143, 143, 143, 125, 78, 78, 28, 78, 13, 1, 1, 1, 1, 1, 1, 1, 143, 143, 201, 201, 201, 201, 201, 201, 201, 193, 193, 193, 193, 143, 125, 125, 78, 28, 28, 1, 143, 143, 143, 143] 201
rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 860
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051757 none C=CC(C)C(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 16, 8, 16, 2, 8, 2, 2, 1, 1, 1, 4, 8, 8, 8, 27, 46, 143, 143, 143, 143, 143, 1, 1, 19, 19, 19, 16, 16, 16, 16, 8, 8, 8, 8, 2, 4, 4, 8, 27, 27, 143, 1, 1, 1, 1] 201
rigid atoms, others: [8, 9, 10, 43, 44, 45, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
total number of confs: 349
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051757 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051757
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051757/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051757
Building REAL300025051758
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051758'
/scratch/stefan/7786831/working/building/REAL300025051758 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051758

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051758/0 /scratch/stefan/7786831/working/building/REAL300025051758 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 639)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/639
`/scratch/stefan/7786831/working/3D/639' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3(CCC3)C2)CC1)

`REAL300025051758.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051758.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051758/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051758 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3(CCC3)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 14, 14, 49, 56, 125, 125, 125, 125, 125, 4, 1, 1, 1, 3, 3, 3, 18, 18, 18, 18, 18, 18, 1, 1, 49, 49, 125, 14, 4, 4, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1] 201
rigid atoms, others: [11, 44, 43, 12, 13, 46, 45, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 328
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051758 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3(CCC3)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [65, 32, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 111, 125, 125, 125, 125, 201, 201, 201, 201, 201, 201, 125, 125, 32, 32, 1, 65, 111, 111, 125, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 125, 125, 125, 125] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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, 45, 46])
total number of confs: 728
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051758 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3(CCC3)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [60, 60, 60, 134, 142, 201, 201, 201, 201, 201, 22, 18, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 18, 18, 134, 134, 201, 60, 22, 22, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 43, 44, 45, 46])
total number of confs: 649
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051758 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051758
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051758/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051758
Building REAL300025051759
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051759'
/scratch/stefan/7786831/working/building/REAL300025051759 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051759

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051759/0 /scratch/stefan/7786831/working/building/REAL300025051759 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 640)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/640
`/scratch/stefan/7786831/working/3D/640' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC#CCCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051759.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051759.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051759/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051759 none CC#CCCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 158, 66, 66, 66, 66, 58, 37, 37, 23, 37, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 201, 201, 201, 190, 194, 181, 181, 158, 158, 66, 58, 58, 37, 23, 23, 1, 66, 66, 66, 66] 201
rigid atoms, others: [39, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 969
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051759 none CC#CCCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [37, 37, 37, 16, 10, 2, 2, 2, 1, 1, 1, 4, 6, 6, 6, 17, 23, 66, 66, 66, 66, 66, 1, 1, 37, 37, 37, 35, 36, 19, 19, 10, 10, 2, 4, 4, 6, 17, 17, 66, 1, 1, 1, 1] 201
rigid atoms, others: [8, 9, 10, 43, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
total number of confs: 313
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051759 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051759
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051759/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051759
Building REAL300025051760
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051760'
/scratch/stefan/7786831/working/building/REAL300025051760 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051760

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051760/0 /scratch/stefan/7786831/working/building/REAL300025051760 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 641)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/641
`/scratch/stefan/7786831/working/3D/641' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@H]2[C@@H]3COC[C@@H]32)CC1)

`REAL300025051760.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051760.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051760/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051760 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@H]2[C@@H]3COC[C@@H]32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 15, 50, 58, 141, 141, 141, 141, 141, 5, 1, 1, 1, 3, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 50, 50, 141, 15, 5, 5, 3, 21, 21, 21, 21, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
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: REAL300025051760 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@H]2[C@@H]3COC[C@@H]32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 12, 1, 1, 1, 1, 1, 1, 1, 72, 72, 123, 141, 141, 141, 141, 201, 201, 201, 201, 201, 201, 201, 201, 141, 141, 32, 32, 1, 72, 123, 123, 141, 201, 201, 201, 201, 141, 141, 141, 141] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 742
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051760 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@H]2[C@@H]3COC[C@@H]32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 137, 145, 201, 201, 201, 201, 201, 30, 21, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 137, 137, 201, 73, 30, 30, 12, 1, 1, 1, 1, 21, 21, 21, 21] 201
rigid atoms, others: [34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 662
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051760 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051760
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051760/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051760
Building REAL300025051761
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051761'
/scratch/stefan/7786831/working/building/REAL300025051761 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051761

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051761/0 /scratch/stefan/7786831/working/building/REAL300025051761 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 642)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/642
`/scratch/stefan/7786831/working/3D/642' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCC1CC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051761.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051761.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051761/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051761 none O=C(CCCC1CC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 10, 16, 24, 38, 38, 1, 1, 1, 4, 6, 6, 6, 20, 25, 66, 66, 66, 66, 66, 1, 1, 10, 10, 19, 19, 24, 24, 38, 38, 38, 38, 38, 2, 4, 4, 6, 20, 20, 66, 1, 1, 1, 1] 201
rigid atoms, others: [8, 9, 10, 43, 44, 45, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
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: REAL300025051761 none O=C(CCCC1CC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 9, 5, 3, 1, 1, 1, 1, 38, 38, 38, 56, 71, 71, 71, 110, 135, 201, 201, 201, 201, 201, 38, 38, 9, 9, 5, 5, 3, 3, 1, 1, 1, 1, 1, 38, 56, 56, 71, 110, 110, 201, 38, 38, 38, 38] 201
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 30, 31] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 647
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051761 none O=C(CCCC1CC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [66, 66, 66, 144, 152, 167, 201, 201, 66, 58, 38, 38, 22, 38, 11, 1, 1, 1, 1, 1, 1, 1, 66, 66, 144, 144, 161, 161, 167, 167, 201, 201, 201, 201, 201, 66, 58, 58, 38, 22, 22, 1, 66, 66, 66, 66] 201
rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 928
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051761 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051761
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051761/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051761
Building REAL300025051762
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051762'
/scratch/stefan/7786831/working/building/REAL300025051762 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051762

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051762/0 /scratch/stefan/7786831/working/building/REAL300025051762 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 643)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/643
`/scratch/stefan/7786831/working/3D/643' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1=O)

`REAL300025051762.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051762.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051762/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051762 none CN1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 8, 8, 2, 2, 2, 1, 1, 1, 7, 28, 28, 28, 67, 80, 182, 182, 182, 182, 182, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 7, 7, 28, 67, 67, 182, 1, 1, 1, 1] 201
rigid atoms, others: [7, 8, 9, 42, 43, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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])
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: REAL300025051762 none CN1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 28, 57, 57, 57, 108, 127, 201, 201, 201, 201, 201, 8, 8, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 8, 28, 28, 57, 108, 108, 201, 8, 8, 8, 8] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 23, 24, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 599
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051762 none CN1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 182, 182, 182, 182, 130, 66, 66, 31, 66, 13, 1, 1, 1, 1, 1, 1, 1, 182, 182, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 182, 130, 130, 66, 31, 31, 1, 182, 182, 182, 182] 201
rigid atoms, others: [39, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 747
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051762 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051762
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051762/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051762
Building REAL300025051763
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051763'
/scratch/stefan/7786831/working/building/REAL300025051763 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051763

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051763/0 /scratch/stefan/7786831/working/building/REAL300025051763 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 644)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/644
`/scratch/stefan/7786831/working/3D/644' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(OCC)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051763.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051763.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051763/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051763 none CCCC(OCC)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 196, 149, 101, 149, 150, 150, 101, 101, 101, 87, 61, 61, 27, 61, 13, 1, 1, 1, 1, 1, 1, 1, 101, 101, 201, 201, 201, 201, 201, 201, 201, 149, 150, 150, 150, 150, 150, 101, 87, 87, 61, 27, 27, 1, 101, 101, 101, 101] 201
rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48])
total number of confs: 988
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051763 none CCCC(OCC)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 15, 5, 2, 5, 8, 8, 2, 2, 1, 1, 1, 4, 9, 9, 9, 26, 42, 101, 101, 101, 101, 101, 1, 1, 17, 17, 17, 17, 17, 16, 16, 5, 8, 8, 8, 8, 8, 2, 4, 4, 9, 26, 26, 101, 1, 1, 1, 1] 201
rigid atoms, others: [9, 10, 11, 45, 46, 47, 48, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 290
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051763 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051763
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051763/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051763
Building REAL300025051764
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051764'
/scratch/stefan/7786831/working/building/REAL300025051764 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051764

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051764/0 /scratch/stefan/7786831/working/building/REAL300025051764 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 645)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/645
`/scratch/stefan/7786831/working/3D/645' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051764.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051764.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051764/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051764 none CC1(C)CCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
194  conformations in input
total number of sets (complete confs): 194
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 22, 22, 22, 94, 113, 182, 182, 182, 182, 182, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 22, 94, 94, 182, 1, 1, 1, 1] 194
rigid atoms, others: [8, 9, 10, 43, 44, 45, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
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: REAL300025051764 none CC1(C)CCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
194  conformations in input
total number of sets (complete confs): 194
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 52, 52, 52, 138, 153, 194, 194, 194, 194, 194, 5, 5, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 5, 12, 12, 52, 138, 138, 194, 5, 5, 5, 5] 194
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 33, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 636
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051764 none CC1(C)CCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 182, 182, 182, 182, 141, 79, 79, 32, 79, 13, 1, 1, 1, 1, 1, 1, 1, 182, 182, 194, 194, 194, 194, 194, 194, 194, 194, 194, 194, 194, 182, 141, 141, 79, 32, 32, 1, 182, 182, 182, 182] 194
rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 725
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051764 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051764
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051764/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051764
Building REAL300025051765
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051765'
/scratch/stefan/7786831/working/building/REAL300025051765 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051765

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051765/0 /scratch/stefan/7786831/working/building/REAL300025051765 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 646)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/646
`/scratch/stefan/7786831/working/3D/646' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=COC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051765.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051765.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051765/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051765 none CC1=COC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 27, 27, 27, 94, 120, 201, 201, 201, 201, 201, 1, 1, 4, 4, 4, 4, 4, 2, 7, 7, 27, 94, 94, 201, 1, 1, 1, 1, 4] 201
rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39])
total number of confs: 550
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051765 none CC1=COC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 12, 32, 32, 32, 98, 123, 201, 201, 201, 201, 201, 4, 4, 1, 2, 2, 2, 1, 4, 12, 12, 32, 98, 98, 201, 4, 4, 4, 4, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 23, 27] set([6, 7, 8, 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, 37, 38])
total number of confs: 561
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051765 none CC1=COC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 141, 56, 56, 30, 56, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 141, 141, 56, 30, 30, 1, 201, 201, 201, 201, 201] 201
rigid atoms, others: [34, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39])
total number of confs: 765
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051765 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051765
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051765/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051765
Building REAL300025051766
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051766'
/scratch/stefan/7786831/working/building/REAL300025051766 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051766

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051766/0 /scratch/stefan/7786831/working/building/REAL300025051766 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 647)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/647
`/scratch/stefan/7786831/working/3D/647' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CSC(=O)N2)CC1)

`REAL300025051766.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051766.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051766/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051766 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CSC(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 14, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
199  conformations in input
total number of sets (complete confs): 199
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 17, 51, 64, 114, 114, 114, 114, 114, 5, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 1, 1, 51, 51, 114, 17, 5, 5, 3, 15, 15, 1, 1, 1, 1] 199
rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 315
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051766 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CSC(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 14, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
199  conformations in input
total number of sets (complete confs): 199
using faster count positions algorithm for large data
unique positions, atoms: [66, 32, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 99, 114, 114, 114, 114, 199, 199, 199, 199, 199, 114, 114, 32, 32, 1, 66, 99, 99, 114, 199, 199, 114, 114, 114, 114] 199
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 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])
total number of confs: 566
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051766 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CSC(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 14, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
199  conformations in input
total number of sets (complete confs): 199
using faster count positions algorithm for large data
unique positions, atoms: [78, 78, 78, 150, 171, 199, 199, 199, 199, 199, 24, 15, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 15, 15, 150, 150, 199, 78, 24, 24, 9, 1, 1, 15, 15, 15, 15] 199
rigid atoms, others: [32, 14, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36])
total number of confs: 687
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051766 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051766
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051766/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051766
Building REAL300025051767
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051767'
/scratch/stefan/7786831/working/building/REAL300025051767 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051767

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051767/0 /scratch/stefan/7786831/working/building/REAL300025051767 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 648)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/648
`/scratch/stefan/7786831/working/3D/648' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(CC)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051767.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051767.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051767/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051767 none C=CC(CC)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 176, 201, 201, 103, 103, 103, 103, 88, 58, 58, 27, 58, 13, 1, 1, 1, 1, 1, 1, 1, 103, 103, 201, 201, 201, 201, 201, 201, 201, 201, 201, 176, 176, 103, 88, 88, 58, 27, 27, 1, 103, 103, 103, 103] 201
rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 880
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051767 none C=CC(CC)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 22, 10, 21, 23, 2, 2, 2, 1, 1, 1, 4, 7, 7, 7, 22, 34, 103, 103, 103, 103, 103, 1, 1, 23, 23, 23, 22, 23, 23, 23, 23, 23, 10, 10, 2, 4, 4, 7, 22, 22, 103, 1, 1, 1, 1] 201
rigid atoms, others: [8, 9, 10, 43, 44, 45, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
total number of confs: 312
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051767 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051767
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051767/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051767
Building REAL300025051768
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051768'
/scratch/stefan/7786831/working/building/REAL300025051768 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051768

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051768/0 /scratch/stefan/7786831/working/building/REAL300025051768 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 649)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/649
`/scratch/stefan/7786831/working/3D/649' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@H]2C[C@H]3C[C@H]3C2)CC1)

`REAL300025051768.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051768.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051768/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051768 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@H]2C[C@H]3C[C@H]3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 19, 54, 65, 140, 140, 140, 140, 140, 5, 1, 1, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 54, 54, 140, 19, 5, 5, 3, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
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: REAL300025051768 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@H]2C[C@H]3C[C@H]3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [67, 32, 12, 1, 1, 1, 1, 1, 1, 1, 67, 67, 123, 139, 139, 139, 139, 201, 201, 201, 201, 201, 201, 201, 201, 139, 139, 32, 32, 1, 67, 123, 123, 139, 201, 201, 201, 201, 201, 201, 139, 139, 139, 139] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 742
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051768 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@H]2C[C@H]3C[C@H]3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 135, 147, 201, 201, 201, 201, 201, 21, 17, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 135, 135, 201, 67, 21, 21, 9, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43])
total number of confs: 643
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051768 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051768
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051768/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051768
Building REAL300025051769
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051769'
/scratch/stefan/7786831/working/building/REAL300025051769 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051769

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051769/0 /scratch/stefan/7786831/working/building/REAL300025051769 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 650)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/650
`/scratch/stefan/7786831/working/3D/650' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=CN1)

`REAL300025051769.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051769.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051769/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051769 none CCCC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=CN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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: [14, 11, 4, 4, 2, 2, 2, 1, 1, 1, 4, 9, 9, 9, 30, 48, 142, 142, 142, 142, 142, 1, 1, 4, 4, 4, 14, 14, 14, 14, 14, 11, 11, 2, 4, 4, 9, 30, 30, 142, 1, 1, 1, 1, 4, 4, 4] 201
rigid atoms, others: [7, 8, 9, 42, 43, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 44, 45, 46])
total number of confs: 328
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051769 none CCCC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=CN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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: [9, 6, 1, 1, 1, 1, 4, 4, 4, 4, 10, 22, 22, 22, 60, 84, 183, 183, 183, 183, 183, 4, 4, 1, 1, 1, 9, 9, 9, 9, 9, 6, 6, 4, 10, 10, 22, 60, 60, 183, 4, 4, 4, 4, 1, 1, 1] 201
rigid atoms, others: [2, 3, 4, 5, 44, 45, 46, 23, 24, 25] set([0, 1, 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, 41, 42, 43])
total number of confs: 471
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051769 none CCCC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=CN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 183, 183, 142, 142, 142, 142, 114, 64, 64, 26, 64, 13, 1, 1, 1, 1, 1, 1, 1, 142, 142, 183, 183, 183, 201, 201, 201, 201, 201, 201, 201, 142, 114, 114, 64, 26, 26, 1, 142, 142, 142, 142, 183, 183, 183] 201
rigid atoms, others: [39, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 747
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051769 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051769
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051769/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051769
Building REAL300025051770
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051770'
/scratch/stefan/7786831/working/building/REAL300025051770 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051770

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051770/0 /scratch/stefan/7786831/working/building/REAL300025051770 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 651)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/651
`/scratch/stefan/7786831/working/3D/651' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=CN1)

`REAL300025051770.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051770.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051770/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051770 none CC(C)C1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=CN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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: [7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 7, 23, 23, 23, 55, 58, 132, 132, 132, 132, 132, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 7, 7, 23, 55, 55, 132, 1, 1, 1, 1, 7, 7, 7] 201
rigid atoms, others: [7, 8, 9, 42, 43, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 44, 45, 46])
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: REAL300025051770 none CC(C)C1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=CN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 23, 62, 62, 62, 123, 128, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 7, 23, 23, 62, 123, 123, 201, 7, 7, 7, 7, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 44, 45, 46, 23, 24, 25, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 634
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051770 none CC(C)C1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=CN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 132, 132, 132, 132, 87, 44, 44, 24, 44, 13, 1, 1, 1, 1, 1, 1, 1, 132, 132, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 132, 87, 87, 44, 24, 24, 1, 132, 132, 132, 132, 201, 201, 201] 201
rigid atoms, others: [39, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 596
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051770 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051770
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051770/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051770
Building REAL300025051771
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051771'
/scratch/stefan/7786831/working/building/REAL300025051771 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051771

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051771/0 /scratch/stefan/7786831/working/building/REAL300025051771 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 652)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/652
`/scratch/stefan/7786831/working/3D/652' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(=O)NC=N1)

`REAL300025051771.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051771.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051771/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051771 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(=O)NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 8, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 2, 2, 2, 1, 1, 1, 6, 24, 24, 24, 72, 88, 174, 174, 174, 174, 174, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 6, 6, 24, 72, 72, 174, 1, 1, 1, 1, 6, 6] 201
rigid atoms, others: [36, 5, 6, 7, 39, 19, 20, 38, 37] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41])
total number of confs: 442
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051771 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(=O)NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 8, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 6, 18, 53, 53, 53, 123, 136, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 2, 2, 2, 6, 18, 18, 53, 123, 123, 201, 6, 6, 6, 6, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 40, 41, 21, 22, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 627
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051771 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(=O)NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 8, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 174, 174, 174, 174, 116, 56, 56, 26, 56, 13, 1, 1, 1, 1, 1, 1, 1, 174, 174, 201, 201, 201, 201, 201, 201, 201, 201, 174, 116, 116, 56, 26, 26, 1, 174, 174, 174, 174, 201, 201] 201
rigid atoms, others: [35, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41])
total number of confs: 686
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051771 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051771
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051771/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051771
Building REAL300025051772
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051772'
/scratch/stefan/7786831/working/building/REAL300025051772 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051772

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051772/0 /scratch/stefan/7786831/working/building/REAL300025051772 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 653)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/653
`/scratch/stefan/7786831/working/3D/653' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=CN1C(C)C)

`REAL300025051772.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051772.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051772/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051772 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=CN1C(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 5, 5, 5, 7, 7, 7, 6, 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, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 2, 2, 2, 1, 1, 1, 6, 13, 13, 13, 50, 76, 154, 154, 154, 154, 154, 1, 1, 7, 7, 7, 7, 10, 10, 7, 7, 7, 2, 6, 6, 13, 50, 50, 154, 1, 1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 10, 10] 201
rigid atoms, others: [37, 6, 7, 40, 39, 19, 20, 38, 5] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 381
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051772 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=CN1C(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 5, 5, 5, 7, 7, 7, 6, 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, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 6, 7, 7, 19, 31, 31, 31, 86, 118, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 3, 3, 2, 2, 2, 7, 19, 19, 31, 86, 86, 201, 7, 7, 7, 7, 1, 1, 3, 4, 4, 4, 4, 4, 4] 201
rigid atoms, others: [0, 1, 2, 3, 41, 42, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 561
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051772 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=CN1C(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 5, 5, 5, 7, 7, 7, 6, 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, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 154, 154, 154, 154, 122, 65, 65, 28, 65, 13, 1, 1, 1, 1, 1, 1, 1, 154, 154, 201, 201, 201, 201, 201, 201, 201, 201, 201, 154, 122, 122, 65, 28, 28, 1, 154, 154, 154, 154, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [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, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 708
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051772 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051772
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051772/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051772
Building REAL300025051773
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051773'
/scratch/stefan/7786831/working/building/REAL300025051773 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051773

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051773/0 /scratch/stefan/7786831/working/building/REAL300025051773 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 654)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/654
`/scratch/stefan/7786831/working/3D/654' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1C)

`REAL300025051773.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051773.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051773/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051773 none CCN1C=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', '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, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 8, 8, 8, 8, 2, 2, 2, 1, 1, 1, 4, 9, 9, 9, 34, 52, 107, 107, 107, 107, 107, 1, 1, 8, 8, 16, 16, 16, 16, 16, 8, 8, 2, 4, 4, 9, 34, 34, 107, 1, 1, 1, 1, 8, 8, 8] 201
rigid atoms, others: [8, 9, 10, 43, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 44, 45, 46])
total number of confs: 300
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051773 none CCN1C=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', '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, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 7, 7, 8, 8, 15, 27, 27, 27, 56, 76, 123, 123, 123, 123, 123, 8, 8, 1, 1, 4, 4, 4, 4, 4, 1, 1, 8, 15, 15, 27, 56, 56, 123, 8, 8, 8, 8, 2, 2, 2] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 24, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 355
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051773 none CCN1C=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', '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, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 123, 123, 123, 123, 107, 107, 107, 107, 93, 60, 60, 26, 60, 13, 1, 1, 1, 1, 1, 1, 1, 107, 107, 123, 123, 201, 201, 201, 201, 201, 123, 123, 107, 93, 93, 60, 26, 26, 1, 107, 107, 107, 107, 123, 123, 123] 201
rigid atoms, others: [39, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 910
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051773 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051773
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051773/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051773
Building REAL300025051774
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051774'
/scratch/stefan/7786831/working/building/REAL300025051774 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051774

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051774/0 /scratch/stefan/7786831/working/building/REAL300025051774 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 655)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/655
`/scratch/stefan/7786831/working/3D/655' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC[N@@H+]1CCCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025051774.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051774.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051774/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051774 none CCC[N@@H+]1CCCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 3, 6, 6, 6, 11, 12, 20, 20, 20, 20, 20, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 6, 11, 11, 20, 1, 1, 1, 1, 3, 3] 20
rigid atoms, others: [11, 12, 13, 49, 50, 51, 52, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 53, 54])
total number of confs: 79
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051774 none CCC[N@@H+]1CCCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 8, 8, 8, 12, 13, 20, 20, 20, 20, 20, 3, 3, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 8, 12, 12, 20, 3, 3, 3, 3, 1, 1] 20
rigid atoms, others: [2, 3, 4, 5, 6, 7, 38, 9, 39, 8, 35, 41, 54, 40, 36, 27, 53, 37] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 71
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051774 none CCC[N@@H+]1CCCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 19, 18, 18, 14, 18, 10, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 19, 19, 18, 14, 14, 1, 20, 20, 20, 20, 20, 20] 20
rigid atoms, others: [48, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54])
total number of confs: 56
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051774 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051774/1 /scratch/stefan/7786831/working/building/REAL300025051774 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 656)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/656
`/scratch/stefan/7786831/working/3D/656' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC[N@H+]1CCCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025051774.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051774.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051774/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051774 none CCC[N@H+]1CCCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [7, 6, 4, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 5, 13, 13, 13, 25, 27, 42, 42, 42, 42, 42, 1, 1, 4, 7, 7, 7, 7, 7, 6, 6, 4, 4, 4, 4, 4, 4, 4, 2, 5, 5, 13, 25, 25, 42, 1, 1, 1, 1, 4, 4] 43
rigid atoms, others: [11, 12, 13, 49, 50, 51, 52, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 53, 54])
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: REAL300025051774 none CCC[N@H+]1CCCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [4, 3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 8, 18, 18, 18, 28, 29, 43, 43, 43, 43, 43, 4, 4, 1, 4, 4, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 18, 28, 28, 43, 4, 4, 4, 4, 1, 1] 43
rigid atoms, others: [2, 3, 4, 5, 6, 7, 38, 9, 39, 8, 35, 41, 54, 40, 36, 27, 53, 37] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 145
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051774 none CCC[N@H+]1CCCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 42, 42, 42, 42, 36, 29, 29, 18, 29, 11, 1, 1, 1, 1, 1, 1, 1, 42, 42, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 42, 36, 36, 29, 18, 18, 1, 42, 42, 42, 42, 43, 43] 43
rigid atoms, others: [48, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54])
total number of confs: 152
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051774 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051774
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051774/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051774/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051774
Building REAL300025051775
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051775'
/scratch/stefan/7786831/working/building/REAL300025051775 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051775

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051775/0 /scratch/stefan/7786831/working/building/REAL300025051775 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 657)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/657
`/scratch/stefan/7786831/working/3D/657' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025051775.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051775.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051775/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051775 none CCOC1CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 28, 20, 20, 20, 10, 2, 2, 2, 1, 1, 1, 3, 6, 6, 6, 22, 33, 92, 92, 92, 92, 92, 1, 1, 20, 28, 28, 28, 28, 28, 20, 20, 20, 20, 10, 10, 2, 3, 3, 6, 22, 22, 92, 1, 1, 1, 1, 20, 20] 201
rigid atoms, others: [9, 10, 11, 44, 45, 46, 47, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49])
total number of confs: 266
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051775 none CCOC1CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 1, 1, 1, 1, 1, 5, 20, 20, 20, 20, 35, 45, 45, 45, 97, 128, 201, 201, 201, 201, 201, 20, 20, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 20, 35, 35, 45, 97, 97, 201, 20, 20, 20, 20, 1, 1] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 34, 48, 49, 25, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 607
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051775 none CCOC1CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 181, 92, 92, 92, 92, 86, 64, 64, 46, 64, 13, 1, 1, 1, 1, 1, 1, 1, 92, 92, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 181, 181, 92, 86, 86, 64, 46, 46, 1, 92, 92, 92, 92, 201, 201] 201
rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49])
total number of confs: 847
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051775 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051775
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051775/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051775
Building REAL300025051776
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051776'
/scratch/stefan/7786831/working/building/REAL300025051776 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051776

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051776/0 /scratch/stefan/7786831/working/building/REAL300025051776 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 658)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/658
`/scratch/stefan/7786831/working/3D/658' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)S1)

`REAL300025051776.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051776.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051776/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051776 none CC1=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', '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, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 30, 30, 30, 88, 104, 196, 196, 196, 196, 196, 1, 1, 4, 4, 4, 4, 4, 4, 2, 7, 7, 30, 88, 88, 196, 1, 1, 1, 1, 4, 4, 4] 201
rigid atoms, others: [35, 36, 37, 6, 7, 8, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41])
total number of confs: 518
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051776 none CC1=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', '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, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 4, 4, 4, 4, 16, 54, 54, 54, 123, 134, 201, 201, 201, 201, 201, 4, 4, 1, 1, 1, 2, 2, 2, 4, 16, 16, 54, 123, 123, 201, 4, 4, 4, 4, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 22, 23, 24] set([5, 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, 36, 37, 38, 39, 40, 41])
total number of confs: 627
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051776 none CC1=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', '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, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 196, 196, 196, 196, 120, 51, 51, 29, 51, 13, 1, 1, 1, 1, 1, 1, 1, 196, 196, 201, 201, 201, 201, 201, 201, 196, 120, 120, 51, 29, 29, 1, 196, 196, 196, 196, 201, 201, 201] 201
rigid atoms, others: [34, 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, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 732
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051776 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051776
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051776/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051776
Building REAL300025051777
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051777'
/scratch/stefan/7786831/working/building/REAL300025051777 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051777

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051777/0 /scratch/stefan/7786831/working/building/REAL300025051777 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 659)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/659
`/scratch/stefan/7786831/working/3D/659' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CON=C2)CC1)

`REAL300025051777.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051777.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051777/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051777 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CON=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 12, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 15, 43, 49, 80, 80, 80, 80, 80, 4, 1, 1, 1, 3, 3, 3, 8, 20, 20, 20, 20, 1, 1, 43, 43, 80, 15, 4, 4, 3, 8, 8, 20, 20, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
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: REAL300025051777 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CON=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 12, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [53, 26, 13, 1, 1, 1, 1, 1, 1, 1, 53, 53, 71, 80, 80, 80, 80, 119, 201, 201, 201, 201, 80, 80, 26, 26, 1, 53, 71, 71, 80, 119, 119, 201, 201, 80, 80, 80, 80] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 661
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051777 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CON=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 12, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [78, 78, 78, 151, 166, 201, 201, 201, 201, 201, 26, 20, 13, 13, 5, 13, 1, 1, 1, 1, 1, 1, 20, 20, 151, 151, 201, 78, 26, 26, 13, 5, 5, 1, 1, 20, 20, 20, 20] 201
rigid atoms, others: [33, 34, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38])
total number of confs: 684
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051777 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051777
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051777/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051777
Building REAL300025051778
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051778'
/scratch/stefan/7786831/working/building/REAL300025051778 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051778

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051778/0 /scratch/stefan/7786831/working/building/REAL300025051778 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 660)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/660
`/scratch/stefan/7786831/working/3D/660' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(=O)CC[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051778.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051778.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051778/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051778 none CN1C(=O)CC[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 5, 5, 2, 5, 2, 2, 1, 1, 1, 5, 22, 22, 22, 80, 111, 165, 165, 165, 165, 165, 1, 1, 5, 5, 5, 5, 5, 5, 5, 2, 5, 5, 22, 80, 80, 165, 1, 1, 1, 1] 182
rigid atoms, others: [43, 40, 41, 10, 11, 12, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 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: REAL300025051778 none CN1C(=O)CC[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 51, 51, 51, 122, 147, 182, 182, 182, 182, 182, 5, 5, 2, 2, 2, 1, 1, 1, 1, 5, 13, 13, 51, 122, 122, 182, 5, 5, 5, 5] 182
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 574
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051778 none CN1C(=O)CC[C@@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [182, 182, 182, 182, 182, 182, 165, 182, 165, 165, 165, 143, 84, 84, 31, 84, 12, 1, 1, 1, 1, 1, 1, 1, 165, 165, 182, 182, 182, 182, 182, 182, 182, 165, 143, 143, 84, 31, 31, 1, 165, 165, 165, 165] 182
rigid atoms, others: [39, 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, 40, 41, 42, 43])
total number of confs: 674
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051778 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051778
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051778/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051778
Building REAL300025051779
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051779'
/scratch/stefan/7786831/working/building/REAL300025051779 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051779

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051779/0 /scratch/stefan/7786831/working/building/REAL300025051779 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 661)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/661
`/scratch/stefan/7786831/working/3D/661' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025051779.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051779.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051779/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051779 none CC1(C)CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 27, 27, 10, 2, 2, 2, 1, 1, 1, 4, 6, 6, 6, 18, 26, 83, 83, 83, 83, 83, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 2, 4, 4, 6, 18, 18, 83, 1, 1, 1, 1, 27, 27] 201
rigid atoms, others: [8, 9, 10, 43, 44, 45, 46, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 47, 48])
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: REAL300025051779 none CC1(C)CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 27, 27, 27, 27, 52, 69, 69, 69, 108, 132, 201, 201, 201, 201, 201, 27, 27, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 6, 6, 27, 52, 52, 69, 108, 108, 201, 27, 27, 27, 27, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 47, 48, 24, 33, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 658
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051779 none CC1(C)CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 168, 83, 83, 83, 83, 73, 44, 44, 24, 44, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 168, 168, 83, 73, 73, 44, 24, 24, 1, 83, 83, 83, 83, 201, 201] 201
rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48])
total number of confs: 850
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051779 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051779
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051779/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051779
Building REAL300025051780
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051780'
/scratch/stefan/7786831/working/building/REAL300025051780 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051780

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051780/0 /scratch/stefan/7786831/working/building/REAL300025051780 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 662)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/662
`/scratch/stefan/7786831/working/3D/662' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3CCCCN23)CC1)

`REAL300025051780.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051780.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051780/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051780 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3CCCCN23)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 5, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 28, 28, 90, 102, 197, 197, 197, 197, 197, 6, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 90, 90, 197, 28, 6, 6, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
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: REAL300025051780 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3CCCCN23)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 5, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [59, 32, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 137, 197, 197, 197, 197, 201, 201, 201, 201, 201, 201, 201, 201, 197, 197, 32, 32, 1, 59, 137, 137, 197, 201, 201, 201, 201, 201, 201, 201, 201, 201, 197, 197, 197, 197] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46])
total number of confs: 716
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051780 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C3CCCCN23)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 5, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [57, 57, 57, 134, 142, 201, 201, 201, 201, 201, 15, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 134, 134, 201, 57, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46])
total number of confs: 648
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051780 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051780
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051780/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051780
Building REAL300025051781
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051781'
/scratch/stefan/7786831/working/building/REAL300025051781 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051781

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051781/0 /scratch/stefan/7786831/working/building/REAL300025051781 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 663)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/663
`/scratch/stefan/7786831/working/3D/663' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)N1C(=O)CC[C@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051781.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051781.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051781/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051781 none CC(C)N1C(=O)CC[C@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 5, 13, 5, 5, 5, 5, 5, 2, 5, 2, 2, 1, 1, 1, 7, 24, 24, 24, 63, 80, 192, 192, 192, 192, 192, 1, 1, 13, 13, 13, 13, 13, 13, 13, 5, 5, 5, 5, 2, 7, 7, 24, 63, 63, 192, 1, 1, 1, 1] 201
rigid atoms, others: [12, 13, 46, 47, 48, 49, 14, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 488
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051781 none CC(C)N1C(=O)CC[C@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 28, 28, 28, 70, 88, 200, 200, 200, 200, 200, 5, 5, 7, 7, 7, 6, 7, 6, 7, 1, 1, 1, 1, 5, 10, 10, 28, 70, 70, 200, 5, 5, 5, 5] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 35, 36, 38, 37] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 510
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051781 none CC(C)N1C(=O)CC[C@H]1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 200, 201, 200, 200, 200, 200, 200, 192, 200, 192, 192, 192, 142, 61, 61, 25, 61, 12, 1, 1, 1, 1, 1, 1, 1, 192, 192, 201, 201, 201, 201, 201, 201, 201, 200, 200, 200, 200, 192, 142, 142, 61, 25, 25, 1, 192, 192, 192, 192] 201
rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49])
total number of confs: 735
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051781 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051781
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051781/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051781
Building REAL300025051782
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051782'
/scratch/stefan/7786831/working/building/REAL300025051782 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051782

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051782/0 /scratch/stefan/7786831/working/building/REAL300025051782 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 664)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/664
`/scratch/stefan/7786831/working/3D/664' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CN=CN=C1)

`REAL300025051782.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051782.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051782/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051782 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CN=CN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 1, 8, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 152, 152, 152, 152, 111, 51, 51, 28, 51, 13, 1, 1, 1, 1, 1, 1, 1, 152, 152, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 152, 111, 111, 51, 28, 28, 1, 152, 152, 152, 152, 201, 201, 201] 201
rigid atoms, others: [36, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 846
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051782 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CN=CN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 1, 8, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 2, 2, 2, 1, 1, 1, 6, 22, 22, 22, 59, 71, 152, 152, 152, 152, 152, 1, 1, 6, 8, 8, 6, 8, 8, 6, 6, 6, 6, 2, 6, 6, 22, 59, 59, 152, 1, 1, 1, 1, 8, 6, 8] 201
rigid atoms, others: [4, 5, 6, 39, 40, 18, 19, 38, 37] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43])
total number of confs: 394
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051782 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CN=CN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 1, 8, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 8, 8, 8, 8, 15, 31, 31, 31, 90, 122, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 4, 4, 4, 3, 8, 15, 15, 31, 90, 90, 201, 8, 8, 8, 8, 1, 1, 1] 201
rigid atoms, others: [1, 41, 42, 43, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 553
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051782 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051782
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051782/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051782
Building REAL300025051783
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051783'
/scratch/stefan/7786831/working/building/REAL300025051783 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051783

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051783/0 /scratch/stefan/7786831/working/building/REAL300025051783 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 665)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/665
`/scratch/stefan/7786831/working/3D/665' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NOC(C2(C(=O)NC3(CNC(=O)CSC4=NNC(=O)[N-]4)CC3)CC2)=C1)

`REAL300025051783.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051783.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051783/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051783 none CC1=NOC(C2(C(=O)NC3(CNC(=O)CSC4=NNC(=O)[N-]4)CC3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 12, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 8, 8, 1, 1, 1, 10, 10, 10, 10, 20, 33, 33, 33, 84, 117, 199, 199, 199, 199, 199, 10, 10, 1, 1, 8, 8, 8, 8, 10, 20, 20, 33, 84, 84, 199, 10, 10, 10, 10, 1, 1, 1, 1, 8] 201
rigid atoms, others: [4, 5, 6, 41, 42, 43, 44, 24, 25] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45])
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: REAL300025051783 none CC1=NOC(C2(C(=O)NC3(CNC(=O)CSC4=NNC(=O)[N-]4)CC3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 12, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 22, 22, 22, 22, 37, 54, 54, 54, 110, 141, 201, 201, 201, 201, 201, 22, 22, 8, 8, 1, 2, 2, 2, 22, 37, 37, 54, 110, 110, 201, 22, 22, 22, 22, 8, 8, 8, 8, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 45, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 644
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051783 none CC1=NOC(C2(C(=O)NC3(CNC(=O)CSC4=NNC(=O)[N-]4)CC3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 12, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 199, 110, 110, 110, 110, 98, 66, 66, 30, 66, 12, 1, 1, 1, 1, 1, 1, 1, 110, 110, 199, 199, 201, 201, 201, 201, 110, 98, 98, 66, 30, 30, 1, 110, 110, 110, 110, 199, 199, 199, 199, 201] 201
rigid atoms, others: [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, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 693
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051783 none CC1=NOC(C2(C(=O)NC3(CNC(=O)CSC4=NNC(=O)[N-]4)CC3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 12, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 22, 10, 2, 2, 2, 1, 1, 1, 4, 8, 8, 8, 27, 44, 110, 110, 110, 110, 110, 1, 1, 10, 10, 22, 22, 22, 22, 2, 4, 4, 8, 27, 27, 110, 1, 1, 1, 1, 10, 10, 10, 10, 22] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 40, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45])
total number of confs: 273
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051783 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051783
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051783/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051783
Building REAL300025051784
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051784'
/scratch/stefan/7786831/working/building/REAL300025051784 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300025051784

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051784/0 /scratch/stefan/7786831/working/building/REAL300025051784 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 666)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/666
`/scratch/stefan/7786831/working/3D/666' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)N1CCOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025051784.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051784.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051784/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051784 none CC(C)N1CCOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 10, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 6, 19, 6, 6, 6, 6, 2, 2, 2, 1, 1, 1, 5, 10, 10, 10, 31, 47, 125, 125, 125, 125, 125, 1, 1, 6, 19, 19, 19, 19, 19, 19, 19, 6, 6, 6, 6, 6, 2, 5, 5, 10, 31, 31, 125, 1, 1, 1, 1, 6, 6] 201
rigid atoms, others: [10, 11, 12, 46, 47, 48, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51])
total number of confs: 316
number of broken/clashed sets: 109
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051784 none CC(C)N1CCOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 10, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 14, 23, 23, 23, 57, 83, 173, 173, 173, 173, 173, 6, 6, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 6, 14, 14, 23, 57, 57, 173, 6, 6, 6, 6, 1, 1] 201
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 50, 35, 36, 26, 38, 51, 37] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 434
number of broken/clashed sets: 109
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051784 none CC(C)N1CCOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 10, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 173, 201, 173, 173, 173, 173, 125, 125, 125, 125, 106, 61, 61, 28, 61, 13, 1, 1, 1, 1, 1, 1, 1, 125, 125, 173, 201, 201, 201, 201, 201, 201, 201, 173, 173, 173, 173, 173, 125, 106, 106, 61, 28, 28, 1, 125, 125, 125, 125, 173, 173] 201
rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51])
total number of confs: 827
number of broken/clashed sets: 109
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051784 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051784/1 /scratch/stefan/7786831/working/building/REAL300025051784 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 667)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/667
`/scratch/stefan/7786831/working/3D/667' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)[N@@H+]1CCOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025051784.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051784.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051784/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051784 none CC(C)[N@@H+]1CCOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [10, 5, 10, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 5, 8, 8, 8, 19, 25, 42, 42, 42, 42, 42, 1, 1, 5, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 5, 2, 5, 5, 8, 19, 19, 42, 1, 1, 1, 1, 5, 5] 45
rigid atoms, others: [11, 12, 13, 47, 48, 49, 50, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52])
total number of confs: 145
number of broken/clashed sets: 45
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051784 none CC(C)[N@@H+]1CCOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 13, 13, 13, 25, 31, 44, 44, 44, 44, 44, 5, 5, 1, 5, 5, 5, 4, 4, 4, 4, 1, 1, 1, 1, 1, 5, 8, 8, 13, 25, 25, 44, 5, 5, 5, 5, 1, 1] 45
rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 9, 39, 8, 35, 52, 36, 27, 51, 37] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 153
number of broken/clashed sets: 45
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051784 none CC(C)[N@@H+]1CCOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [45, 44, 45, 44, 44, 44, 44, 44, 42, 42, 42, 42, 40, 35, 35, 23, 35, 12, 1, 1, 1, 1, 1, 1, 1, 42, 42, 44, 45, 45, 45, 45, 45, 45, 45, 44, 44, 44, 44, 44, 42, 40, 40, 35, 23, 23, 1, 42, 42, 42, 42, 44, 44] 45
rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52])
total number of confs: 160
number of broken/clashed sets: 45
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051784 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `2'
/scratch/stefan/7786831/working/building/REAL300025051784/2 /scratch/stefan/7786831/working/building/REAL300025051784 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 2 (index: 668)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/668
`/scratch/stefan/7786831/working/3D/668' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)[N@H+]1CCOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025051784.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300025051784.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051784/2/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`2.mol2' -> `2.mol2.original'
`output.mol2' -> `2.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051784 none CC(C)[N@H+]1CCOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [8, 5, 8, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 5, 8, 8, 8, 19, 25, 40, 40, 40, 40, 40, 1, 1, 5, 8, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 2, 5, 5, 8, 19, 19, 40, 1, 1, 1, 1, 5, 5] 43
rigid atoms, others: [11, 12, 13, 47, 48, 49, 50, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52])
total number of confs: 137
number of broken/clashed sets: 43
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051784 none CC(C)[N@H+]1CCOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 13, 13, 13, 25, 30, 42, 42, 42, 42, 42, 5, 5, 1, 5, 5, 5, 4, 4, 4, 4, 1, 1, 1, 1, 1, 5, 8, 8, 13, 25, 25, 42, 5, 5, 5, 5, 1, 1] 43
rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 9, 39, 8, 35, 52, 36, 27, 51, 37] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 149
number of broken/clashed sets: 43
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051784 none CC(C)[N@H+]1CCOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [43, 42, 43, 42, 42, 42, 42, 42, 40, 40, 40, 40, 39, 35, 35, 22, 35, 12, 1, 1, 1, 1, 1, 1, 1, 40, 40, 42, 43, 43, 43, 43, 43, 43, 43, 42, 42, 42, 42, 42, 40, 39, 39, 35, 22, 22, 1, 40, 40, 40, 40, 42, 42] 43
rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52])
total number of confs: 149
number of broken/clashed sets: 43
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051784 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051784
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
2: /scratch/stefan/7786831/working/building/REAL300025051784/2.*
1: /scratch/stefan/7786831/working/building/REAL300025051784/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051784/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051784
Building REAL300025051785
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051785'
/scratch/stefan/7786831/working/building/REAL300025051785 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051785

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051785/0 /scratch/stefan/7786831/working/building/REAL300025051785 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 669)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/669
`/scratch/stefan/7786831/working/3D/669' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CNC(=O)C=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051785.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051785.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051785/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051785 none O=C(CCC1=CNC(=O)C=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 11, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 9, 11, 21, 21, 21, 21, 21, 21, 1, 1, 1, 6, 10, 10, 10, 25, 37, 89, 89, 89, 89, 89, 1, 1, 9, 9, 11, 11, 21, 21, 21, 21, 2, 6, 6, 10, 25, 25, 89, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 252
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051785 none O=C(CCC1=CNC(=O)C=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 11, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 46, 63, 63, 63, 109, 136, 201, 201, 201, 201, 201, 21, 21, 7, 7, 3, 3, 1, 1, 1, 1, 21, 46, 46, 63, 109, 109, 201, 21, 21, 21, 21] 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, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051785 none O=C(CCC1=CNC(=O)C=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 11, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [89, 89, 89, 141, 142, 201, 201, 201, 201, 201, 201, 89, 77, 43, 43, 25, 43, 12, 1, 1, 1, 1, 1, 1, 1, 89, 89, 141, 141, 142, 142, 201, 201, 201, 201, 89, 77, 77, 43, 25, 25, 1, 89, 89, 89, 89] 201
rigid atoms, others: [41, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 736
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051785 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051785
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051785/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051785
Building REAL300025051786
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051786'
/scratch/stefan/7786831/working/building/REAL300025051786 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051786

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051786/0 /scratch/stefan/7786831/working/building/REAL300025051786 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 670)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/670
`/scratch/stefan/7786831/working/3D/670' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2(F)CCOC2)CC1)

`REAL300025051786.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051786.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051786/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051786 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2(F)CCOC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 12, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 27, 86, 99, 184, 184, 184, 184, 184, 6, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 1, 1, 86, 86, 184, 27, 6, 6, 3, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 490
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051786 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2(F)CCOC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 12, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 31, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 139, 184, 184, 184, 184, 201, 201, 201, 201, 201, 184, 184, 31, 31, 1, 66, 139, 139, 184, 201, 201, 201, 201, 201, 201, 184, 184, 184, 184] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 757
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051786 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2(F)CCOC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 12, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 61, 61, 134, 144, 201, 201, 201, 201, 201, 17, 10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 134, 134, 201, 61, 17, 17, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10] 201
rigid atoms, others: [32, 33, 34, 35, 36, 14, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40])
total number of confs: 631
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051786 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051786
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051786/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051786
Building REAL300025051787
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051787'
/scratch/stefan/7786831/working/building/REAL300025051787 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051787

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051787/0 /scratch/stefan/7786831/working/building/REAL300025051787 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 671)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/671
`/scratch/stefan/7786831/working/3D/671' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=C1)

`REAL300025051787.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051787.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051787/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051787 none COC1=CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 7, 7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 7, 20, 20, 20, 64, 89, 179, 179, 179, 179, 179, 1, 1, 7, 7, 9, 9, 9, 7, 7, 7, 7, 2, 7, 7, 20, 64, 64, 179, 1, 1, 1, 1, 7] 201
rigid atoms, others: [43, 9, 10, 11, 44, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45])
total number of confs: 446
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051787 none COC1=CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 7, 17, 38, 38, 38, 88, 113, 201, 201, 201, 201, 201, 7, 7, 1, 1, 3, 3, 3, 1, 1, 3, 3, 7, 17, 17, 38, 88, 88, 201, 7, 7, 7, 7, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 45, 25, 26, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 528
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051787 none COC1=CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 179, 179, 179, 179, 161, 103, 103, 55, 103, 13, 1, 1, 1, 1, 1, 1, 1, 179, 179, 201, 201, 201, 201, 201, 201, 201, 201, 201, 179, 161, 161, 103, 55, 55, 1, 179, 179, 179, 179, 201] 201
rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45])
total number of confs: 811
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051787 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051787
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051787/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051787
Building REAL300025051788
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051788'
/scratch/stefan/7786831/working/building/REAL300025051788 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051788

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051788/0 /scratch/stefan/7786831/working/building/REAL300025051788 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 672)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/672
`/scratch/stefan/7786831/working/3D/672' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC(Cl)=CS2)CC1)

`REAL300025051788.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051788.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051788/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051788 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC(Cl)=CS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'Cl', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 16, 1, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 30, 101, 109, 197, 197, 197, 197, 197, 6, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 1, 101, 101, 197, 30, 6, 6, 3, 8, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 537
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051788 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC(Cl)=CS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'Cl', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 16, 1, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [57, 33, 13, 1, 1, 1, 1, 1, 1, 1, 57, 57, 134, 197, 197, 197, 197, 201, 201, 201, 201, 201, 197, 197, 33, 33, 1, 57, 134, 134, 197, 201, 197, 197, 197, 197] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 730
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051788 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC(Cl)=CS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'Cl', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 16, 1, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [53, 53, 53, 135, 139, 201, 201, 201, 201, 201, 15, 8, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 8, 135, 135, 201, 53, 15, 15, 5, 1, 8, 8, 8, 8] 201
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 635
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051788 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051788
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051788/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051788
Building REAL300025051789
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051789'
/scratch/stefan/7786831/working/building/REAL300025051789 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051789

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051789/0 /scratch/stefan/7786831/working/building/REAL300025051789 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 673)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/673
`/scratch/stefan/7786831/working/3D/673' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCCC2(F)F)CC1)

`REAL300025051789.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051789.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051789/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051789 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCCC2(F)F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 31, 41, 115, 115, 115, 115, 115, 5, 1, 1, 1, 3, 3, 3, 19, 40, 40, 40, 40, 40, 40, 1, 1, 31, 31, 115, 13, 5, 5, 3, 19, 19, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
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: REAL300025051789 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCCC2(F)F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [68, 33, 13, 1, 1, 1, 1, 1, 1, 1, 68, 68, 97, 115, 115, 115, 115, 187, 201, 201, 201, 201, 201, 201, 115, 115, 33, 33, 1, 68, 97, 97, 115, 187, 187, 201, 201, 201, 201, 201, 201, 201, 115, 115, 115, 115] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 820
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051789 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCCC2(F)F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [94, 94, 94, 142, 152, 201, 201, 201, 201, 201, 52, 40, 29, 29, 6, 29, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 142, 142, 201, 94, 52, 52, 29, 6, 6, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40] 201
rigid atoms, others: [35, 36, 37, 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, 42, 43, 44, 45])
total number of confs: 693
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051789 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051789
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051789/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051789
Building REAL300025051790
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051790'
/scratch/stefan/7786831/working/building/REAL300025051790 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051790

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051790/0 /scratch/stefan/7786831/working/building/REAL300025051790 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 674)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/674
`/scratch/stefan/7786831/working/3D/674' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N1C)

`REAL300025051790.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051790.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051790/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051790 none CC1=NC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 7, 30, 30, 30, 80, 94, 174, 176, 176, 176, 176, 1, 1, 7, 7, 7, 7, 7, 7, 2, 7, 7, 30, 80, 80, 176, 1, 1, 1, 1, 7, 7, 7] 201
rigid atoms, others: [36, 37, 38, 7, 8, 9, 39, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42])
total number of confs: 469
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051790 none CC1=NC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 7, 7, 23, 59, 59, 59, 121, 132, 201, 201, 201, 201, 201, 7, 7, 1, 1, 2, 2, 2, 1, 7, 23, 23, 59, 121, 121, 201, 7, 7, 7, 7, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 23, 24, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 619
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051790 none CC1=NC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 176, 176, 176, 176, 126, 61, 61, 29, 61, 13, 1, 1, 1, 1, 1, 1, 1, 176, 176, 201, 201, 201, 201, 201, 201, 176, 126, 126, 61, 29, 29, 1, 176, 176, 176, 176, 201, 201, 201] 201
rigid atoms, others: [35, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 701
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051790 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051790
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051790/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051790
Building REAL300025051791
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051791'
/scratch/stefan/7786831/working/building/REAL300025051791 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051791

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051791/0 /scratch/stefan/7786831/working/building/REAL300025051791 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 675)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/675
`/scratch/stefan/7786831/working/3D/675' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CC=C(F)C=N2)CC1)

`REAL300025051791.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051791.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051791/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051791 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CC=C(F)C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 15, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 15, 36, 38, 87, 87, 87, 87, 87, 5, 1, 1, 1, 3, 3, 3, 22, 38, 38, 38, 38, 38, 38, 1, 1, 36, 36, 87, 15, 5, 5, 3, 22, 22, 38, 38, 38, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
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: REAL300025051791 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CC=C(F)C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 15, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [41, 26, 13, 1, 1, 1, 1, 1, 1, 1, 41, 41, 76, 87, 87, 87, 87, 189, 201, 201, 201, 201, 201, 201, 87, 87, 26, 26, 1, 41, 76, 76, 87, 189, 189, 201, 201, 201, 87, 87, 87, 87] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 770
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051791 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CC=C(F)C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 15, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [112, 112, 112, 182, 182, 201, 201, 201, 201, 201, 49, 38, 30, 30, 7, 30, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 182, 182, 201, 112, 49, 49, 30, 7, 7, 1, 1, 1, 38, 38, 38, 38] 201
rigid atoms, others: [35, 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, 38, 39, 40, 41])
total number of confs: 781
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051791 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051791
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051791/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051791
Building REAL300025051792
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051792'
/scratch/stefan/7786831/working/building/REAL300025051792 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051792

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051792/0 /scratch/stefan/7786831/working/building/REAL300025051792 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 676)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/676
`/scratch/stefan/7786831/working/3D/676' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3=CC=C(F)C=C32)CC1)

`REAL300025051792.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051792.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051792/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051792 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3=CC=C(F)C=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 18, 57, 64, 139, 139, 139, 139, 139, 5, 1, 1, 1, 3, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 57, 57, 139, 18, 5, 5, 3, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
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: REAL300025051792 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3=CC=C(F)C=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [66, 31, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 121, 139, 139, 139, 139, 201, 201, 201, 201, 201, 201, 201, 201, 139, 139, 31, 31, 1, 66, 121, 121, 139, 201, 201, 201, 201, 201, 201, 139, 139, 139, 139] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 723
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051792 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3=CC=C(F)C=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [66, 66, 66, 131, 141, 201, 201, 201, 201, 201, 28, 18, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 131, 131, 201, 66, 28, 28, 11, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43])
total number of confs: 659
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051792 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051792
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051792/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051792
Building REAL300025051793
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051793'
/scratch/stefan/7786831/working/building/REAL300025051793 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051793

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051793/0 /scratch/stefan/7786831/working/building/REAL300025051793 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 677)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/677
`/scratch/stefan/7786831/working/3D/677' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C(C3CC3)OC=C2)CC1)

`REAL300025051793.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051793.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051793/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051793 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C(C3CC3)OC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 12, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 10, 10, 21, 27, 63, 63, 63, 63, 63, 5, 1, 1, 1, 3, 3, 3, 16, 16, 44, 44, 16, 16, 16, 1, 1, 21, 21, 63, 10, 5, 5, 3, 44, 44, 44, 44, 44, 16, 16, 1, 1, 1, 1] 153
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 252
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051793 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C(C3CC3)OC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 12, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [42, 22, 13, 1, 1, 1, 1, 1, 1, 1, 42, 42, 59, 63, 63, 63, 63, 117, 117, 153, 153, 117, 117, 117, 63, 63, 22, 22, 1, 42, 59, 59, 63, 153, 153, 153, 153, 153, 117, 117, 63, 63, 63, 63] 153
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 474
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051793 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C(C3CC3)OC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 12, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [85, 85, 85, 115, 125, 153, 153, 153, 153, 153, 54, 44, 35, 35, 7, 35, 7, 1, 1, 1, 1, 7, 7, 7, 44, 44, 115, 115, 153, 85, 54, 54, 35, 1, 1, 1, 1, 1, 7, 7, 44, 44, 44, 44] 153
rigid atoms, others: [33, 34, 35, 36, 37, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43])
total number of confs: 522
number of broken/clashed sets: 1
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051793 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C(C3CC3)OC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 12, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [46, 46, 46, 73, 81, 117, 117, 117, 117, 117, 23, 16, 10, 10, 1, 10, 1, 1, 1, 7, 7, 1, 1, 1, 16, 16, 73, 73, 117, 46, 23, 23, 10, 7, 7, 7, 7, 7, 1, 1, 16, 16, 16, 16] 153
rigid atoms, others: [38, 39, 14, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43])
total number of confs: 403
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051793 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051793
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051793/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051793
Building REAL300025051794
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051794'
/scratch/stefan/7786831/working/building/REAL300025051794 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051794

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051794/0 /scratch/stefan/7786831/working/building/REAL300025051794 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 678)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/678
`/scratch/stefan/7786831/working/3D/678' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=COC(C(F)F)=C2)CC1)

`REAL300025051794.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051794.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051794/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051794 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=COC(C(F)F)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'F', 'F', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 12, 1, 5, 15, 15, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 32, 39, 94, 94, 94, 94, 94, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 48, 48, 9, 1, 1, 32, 32, 94, 11, 5, 5, 3, 9, 48, 9, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 364
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051794 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=COC(C(F)F)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'F', 'F', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 12, 1, 5, 15, 15, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 33, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 83, 94, 94, 94, 94, 173, 173, 173, 173, 201, 201, 173, 94, 94, 33, 33, 1, 61, 83, 83, 94, 173, 201, 173, 94, 94, 94, 94] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 655
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051794 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=COC(C(F)F)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'F', 'F', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 12, 1, 5, 15, 15, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [32, 32, 32, 75, 91, 173, 173, 173, 173, 173, 15, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 11, 11, 1, 9, 9, 75, 75, 173, 32, 15, 15, 5, 1, 11, 1, 9, 9, 9, 9] 201
rigid atoms, others: [33, 35, 14, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 36, 37, 38, 39])
total number of confs: 490
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051794 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051794
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051794/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051794
Building REAL300025051795
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051795'
/scratch/stefan/7786831/working/building/REAL300025051795 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051795

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051795/0 /scratch/stefan/7786831/working/building/REAL300025051795 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 679)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/679
`/scratch/stefan/7786831/working/3D/679' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(C(F)F)=NC=N2)CC1)

`REAL300025051795.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051795.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051795/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051795 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(C(F)F)=NC=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 5, 15, 15, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
124  conformations in input
total number of sets (complete confs): 124
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 30, 36, 74, 74, 74, 74, 74, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 40, 40, 9, 9, 9, 1, 1, 30, 30, 74, 13, 5, 5, 3, 9, 40, 9, 1, 1, 1, 1] 124
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
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: REAL300025051795 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(C(F)F)=NC=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 5, 15, 15, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
124  conformations in input
total number of sets (complete confs): 124
using faster count positions algorithm for large data
unique positions, atoms: [42, 22, 13, 1, 1, 1, 1, 1, 1, 1, 42, 42, 69, 74, 74, 74, 74, 124, 124, 124, 124, 124, 124, 124, 124, 74, 74, 22, 22, 1, 42, 69, 69, 74, 124, 124, 124, 74, 74, 74, 74] 124
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 377
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051795 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(C(F)F)=NC=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 5, 15, 15, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
124  conformations in input
total number of sets (complete confs): 124
using faster count positions algorithm for large data
unique positions, atoms: [36, 36, 36, 63, 71, 124, 124, 124, 124, 124, 15, 9, 6, 5, 1, 5, 1, 1, 1, 1, 10, 10, 1, 1, 1, 9, 9, 63, 63, 124, 36, 15, 15, 6, 1, 10, 1, 9, 9, 9, 9] 124
rigid atoms, others: [34, 36, 14, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 37, 38, 39, 40])
total number of confs: 388
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051795 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051795
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051795/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051795
Building REAL300025051796
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051796'
/scratch/stefan/7786831/working/building/REAL300025051796 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051796

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051796/0 /scratch/stefan/7786831/working/building/REAL300025051796 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 680)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/680
`/scratch/stefan/7786831/working/3D/680' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2=CSC=C2)CC1)

`REAL300025051796.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051796.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051796/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051796 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2=CSC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 14, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 32, 36, 60, 60, 60, 60, 60, 5, 1, 1, 1, 3, 3, 3, 21, 21, 21, 21, 21, 59, 59, 59, 59, 1, 1, 32, 32, 60, 13, 5, 5, 3, 21, 21, 59, 59, 59, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 273
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051796 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2=CSC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 14, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 21, 12, 1, 1, 1, 1, 1, 1, 1, 30, 30, 52, 60, 60, 60, 60, 119, 119, 119, 119, 119, 201, 201, 201, 201, 60, 60, 21, 21, 1, 30, 52, 52, 60, 119, 119, 201, 201, 201, 60, 60, 60, 60] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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])
total number of confs: 575
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051796 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2=CSC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 14, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [126, 126, 126, 191, 195, 201, 201, 201, 201, 201, 71, 59, 41, 41, 9, 41, 9, 9, 9, 1, 9, 1, 1, 1, 1, 1, 59, 59, 191, 191, 201, 126, 71, 71, 41, 9, 9, 1, 1, 1, 59, 59, 59, 59] 201
rigid atoms, others: [37, 38, 39, 19, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43])
total number of confs: 765
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051796 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2=CSC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 14, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [63, 63, 63, 104, 108, 119, 119, 119, 119, 119, 27, 21, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 21, 21, 104, 104, 119, 63, 27, 27, 12, 1, 1, 9, 9, 9, 21, 21, 21, 21] 201
rigid atoms, others: [35, 36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 456
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051796 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051796
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051796/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051796
Building REAL300025051797
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051797'
/scratch/stefan/7786831/working/building/REAL300025051797 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051797

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051797/0 /scratch/stefan/7786831/working/building/REAL300025051797 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 681)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/681
`/scratch/stefan/7786831/working/3D/681' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1C)

`REAL300025051797.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051797.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051797/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051797 none COC1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 7, 7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 7, 11, 11, 11, 40, 62, 158, 158, 158, 158, 158, 1, 1, 7, 7, 16, 16, 16, 7, 7, 2, 7, 7, 11, 40, 40, 158, 1, 1, 1, 1, 7, 7, 7] 201
rigid atoms, others: [39, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45])
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: REAL300025051797 none COC1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 7, 7, 7, 7, 19, 30, 30, 30, 75, 108, 201, 201, 201, 201, 201, 7, 7, 1, 1, 4, 4, 4, 1, 1, 7, 19, 19, 30, 75, 75, 201, 7, 7, 7, 7, 2, 2, 2] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 25, 26, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 534
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051797 none COC1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 158, 158, 158, 158, 130, 75, 75, 31, 75, 13, 1, 1, 1, 1, 1, 1, 1, 158, 158, 201, 201, 201, 201, 201, 201, 201, 158, 130, 130, 75, 31, 31, 1, 158, 158, 158, 158, 201, 201, 201] 201
rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 693
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051797 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051797
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051797/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051797
Building REAL300025051798
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051798'
/scratch/stefan/7786831/working/building/REAL300025051798 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051798

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051798/0 /scratch/stefan/7786831/working/building/REAL300025051798 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 682)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/682
`/scratch/stefan/7786831/working/3D/682' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN3CCOCC3=N2)CC1)

`REAL300025051798.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051798.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051798/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051798 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN3CCOCC3=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', '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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 12, 5, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 31, 31, 100, 111, 199, 199, 199, 199, 199, 7, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 100, 100, 199, 31, 7, 7, 3, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 42, 11, 12, 13, 44, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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])
total number of confs: 545
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051798 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN3CCOCC3=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', '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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 12, 5, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 151, 199, 199, 199, 199, 201, 201, 201, 201, 201, 201, 201, 201, 199, 199, 32, 32, 1, 69, 151, 151, 199, 201, 201, 201, 201, 201, 201, 201, 199, 199, 199, 199] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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: 733
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051798 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN3CCOCC3=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', '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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 12, 5, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 48, 125, 135, 201, 201, 201, 201, 201, 13, 6, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 125, 125, 201, 48, 13, 13, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44])
total number of confs: 619
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051798 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051798
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051798/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051798
Building REAL300025051799
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051799'
/scratch/stefan/7786831/working/building/REAL300025051799 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051799

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051799/0 /scratch/stefan/7786831/working/building/REAL300025051799 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 683)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/683
`/scratch/stefan/7786831/working/3D/683' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=CS1)

`REAL300025051799.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051799.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051799/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051799 none COCC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 18, 10, 10, 2, 2, 2, 1, 1, 1, 3, 8, 8, 8, 27, 47, 119, 119, 119, 119, 119, 1, 1, 10, 10, 10, 30, 30, 30, 18, 18, 2, 3, 3, 8, 27, 27, 119, 1, 1, 1, 1, 10, 10] 201
rigid atoms, others: [38, 7, 8, 9, 39, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 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: REAL300025051799 none COCC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 10, 10, 10, 10, 17, 30, 30, 30, 75, 106, 191, 191, 191, 191, 191, 10, 10, 1, 1, 1, 12, 12, 12, 6, 6, 10, 17, 17, 30, 75, 75, 191, 10, 10, 10, 10, 1, 1] 201
rigid atoms, others: [2, 3, 4, 5, 42, 43, 23, 24, 25] set([0, 1, 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, 41])
total number of confs: 539
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051799 none COCC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 191, 191, 119, 119, 119, 119, 98, 64, 64, 29, 64, 13, 1, 1, 1, 1, 1, 1, 1, 119, 119, 191, 191, 191, 201, 201, 201, 201, 201, 119, 98, 98, 64, 29, 29, 1, 119, 119, 119, 119, 191, 191] 201
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43])
total number of confs: 644
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051799 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051799
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051799/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051799
Building REAL300025051800
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051800'
/scratch/stefan/7786831/working/building/REAL300025051800 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051800

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051800/0 /scratch/stefan/7786831/working/building/REAL300025051800 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 684)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/684
`/scratch/stefan/7786831/working/3D/684' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=CNC=CC3=N2)CC1)

`REAL300025051800.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051800.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051800/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051800 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=CNC=CC3=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 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: [30, 30, 30, 103, 114, 201, 201, 201, 201, 201, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 103, 103, 201, 30, 6, 6, 3, 7, 7, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 551
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051800 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=CNC=CC3=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 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: [62, 30, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 153, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 30, 30, 1, 62, 153, 153, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 754
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051800 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=CNC=CC3=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 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: [44, 44, 44, 128, 137, 201, 201, 201, 201, 201, 11, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 128, 128, 201, 44, 11, 11, 4, 1, 1, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42])
total number of confs: 610
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051800 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051800
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051800/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051800
Building REAL300025051801
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051801'
/scratch/stefan/7786831/working/building/REAL300025051801 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051801

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051801/0 /scratch/stefan/7786831/working/building/REAL300025051801 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 685)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/685
`/scratch/stefan/7786831/working/3D/685' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)S1)

`REAL300025051801.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051801.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051801/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051801 none CC1=NC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', '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, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 8, 2, 2, 2, 1, 1, 1, 7, 18, 18, 18, 62, 74, 157, 157, 157, 157, 157, 1, 1, 10, 10, 10, 10, 10, 10, 8, 8, 2, 7, 7, 18, 62, 62, 157, 1, 1, 1, 1, 10, 10, 10] 201
rigid atoms, others: [38, 7, 8, 9, 39, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 42, 43, 44])
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: REAL300025051801 none CC1=NC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', '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, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 4, 10, 10, 10, 10, 26, 44, 44, 44, 104, 115, 201, 201, 201, 201, 201, 10, 10, 1, 1, 1, 2, 2, 2, 4, 4, 10, 26, 26, 44, 104, 104, 201, 10, 10, 10, 10, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25] set([5, 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, 41, 42, 43, 44])
total number of confs: 603
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051801 none CC1=NC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(C)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', '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, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 199, 157, 157, 157, 157, 112, 60, 60, 29, 60, 13, 1, 1, 1, 1, 1, 1, 1, 157, 157, 201, 201, 201, 201, 201, 201, 199, 199, 157, 112, 112, 60, 29, 29, 1, 157, 157, 157, 157, 201, 201, 201] 201
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 816
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051801 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051801
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051801/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051801
Building REAL300025051802
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051802'
/scratch/stefan/7786831/working/building/REAL300025051802 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051802

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051802/0 /scratch/stefan/7786831/working/building/REAL300025051802 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 686)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/686
`/scratch/stefan/7786831/working/3D/686' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1Cl)

`REAL300025051802.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051802.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051802/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051802 none CN1N=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'Cl', '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, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 16, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 6, 2, 2, 2, 1, 1, 1, 4, 21, 21, 21, 80, 92, 157, 157, 157, 157, 157, 1, 1, 6, 6, 6, 6, 6, 6, 2, 4, 4, 21, 80, 80, 157, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 7, 8, 9, 39, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 424
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051802 none CN1N=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'Cl', '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, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 16, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 14, 53, 53, 53, 139, 154, 201, 201, 201, 201, 201, 6, 6, 1, 1, 2, 2, 2, 1, 6, 14, 14, 53, 139, 139, 201, 6, 6, 6, 6] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 23, 24, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 647
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051802 none CN1N=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'Cl', '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, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 16, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 157, 157, 157, 157, 126, 65, 65, 26, 65, 13, 1, 1, 1, 1, 1, 1, 1, 157, 157, 201, 201, 201, 201, 201, 201, 157, 126, 126, 65, 26, 26, 1, 157, 157, 157, 157] 201
rigid atoms, others: [35, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39])
total number of confs: 660
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051802 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051802
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051802/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051802
Building REAL300025051803
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051803'
/scratch/stefan/7786831/working/building/REAL300025051803 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051803

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051803/0 /scratch/stefan/7786831/working/building/REAL300025051803 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 687)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/687
`/scratch/stefan/7786831/working/3D/687' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N1)

`REAL300025051803.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051803.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051803/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051803 none CC1=CC(C)=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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: [8, 8, 8, 8, 8, 2, 2, 2, 1, 1, 1, 7, 25, 25, 25, 60, 74, 148, 148, 148, 148, 148, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 2, 7, 7, 25, 60, 60, 148, 1, 1, 1, 1, 8] 201
rigid atoms, others: [39, 8, 9, 10, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 43])
total number of confs: 382
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051803 none CC1=CC(C)=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 20, 51, 51, 51, 111, 127, 201, 201, 201, 201, 201, 8, 8, 1, 2, 2, 2, 1, 2, 2, 2, 8, 20, 20, 51, 111, 111, 201, 8, 8, 8, 8, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 43, 24, 28] set([7, 8, 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, 42])
total number of confs: 605
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051803 none CC1=CC(C)=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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, 201, 201, 148, 148, 148, 148, 101, 53, 53, 27, 53, 13, 1, 1, 1, 1, 1, 1, 1, 148, 148, 201, 201, 201, 201, 201, 201, 201, 201, 148, 101, 101, 53, 27, 27, 1, 148, 148, 148, 148, 201] 201
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42, 43])
total number of confs: 654
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051803 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051803
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051803/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051803
Building REAL300025051804
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051804'
/scratch/stefan/7786831/working/building/REAL300025051804 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051804

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051804/0 /scratch/stefan/7786831/working/building/REAL300025051804 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 688)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/688
`/scratch/stefan/7786831/working/3D/688' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=C(F)C=C2F)CC1)

`REAL300025051804.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051804.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051804/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051804 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=C(F)C=C2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 15, 1, 1, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 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: [30, 30, 30, 96, 110, 192, 192, 192, 192, 192, 7, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 1, 1, 96, 96, 192, 30, 7, 7, 3, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34])
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: REAL300025051804 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=C(F)C=C2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 15, 1, 1, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 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: [69, 30, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 148, 192, 192, 192, 192, 201, 201, 201, 201, 201, 201, 201, 192, 192, 30, 30, 1, 69, 148, 148, 192, 201, 201, 192, 192, 192, 192] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 724
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051804 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=C(F)C=C2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 15, 1, 1, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 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: [56, 56, 56, 139, 148, 201, 201, 201, 201, 201, 14, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 139, 139, 201, 56, 14, 14, 4, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [33, 34, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38])
total number of confs: 630
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051804 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051804
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051804/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051804
Building REAL300025051805
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051805'
/scratch/stefan/7786831/working/building/REAL300025051805 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051805

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051805/0 /scratch/stefan/7786831/working/building/REAL300025051805 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 689)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/689
`/scratch/stefan/7786831/working/3D/689' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)S(C)(=O)=O)

`REAL300025051805.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051805.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051805/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051805 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)S(C)(=O)=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
175  conformations in input
total number of sets (complete confs): 175
using faster count positions algorithm for large data
unique positions, atoms: [169, 118, 118, 118, 118, 103, 71, 71, 34, 71, 13, 1, 1, 1, 1, 1, 1, 1, 118, 118, 169, 175, 175, 175, 169, 169, 169, 169, 118, 103, 103, 71, 34, 34, 1, 118, 118, 118, 118, 175, 175, 175] 175
rigid atoms, others: [34, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41])
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: REAL300025051805 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)S(C)(=O)=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
175  conformations in input
total number of sets (complete confs): 175
using faster count positions algorithm for large data
unique positions, atoms: [9, 2, 2, 2, 1, 1, 1, 4, 16, 16, 16, 42, 50, 118, 118, 118, 118, 118, 1, 1, 9, 20, 20, 20, 9, 9, 9, 9, 2, 4, 4, 16, 42, 42, 118, 1, 1, 1, 1, 20, 20, 20] 175
rigid atoms, others: [35, 4, 5, 6, 18, 19, 36, 38, 37] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41])
total number of confs: 352
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051805 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051805
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051805/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051805
Building REAL300025051806
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051806'
/scratch/stefan/7786831/working/building/REAL300025051806 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051806

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051806/0 /scratch/stefan/7786831/working/building/REAL300025051806 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 690)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/690
`/scratch/stefan/7786831/working/3D/690' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051806.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051806.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051806/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051806 none CS(=O)(=O)CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 14, 11, 11, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 165, 165, 165, 165, 139, 74, 74, 32, 74, 13, 1, 1, 1, 1, 1, 1, 1, 165, 165, 201, 201, 201, 201, 201, 201, 201, 165, 139, 139, 74, 32, 32, 1, 165, 165, 165, 165] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41])
total number of confs: 832
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051806 none CS(=O)(=O)CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 14, 11, 11, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 11, 19, 19, 8, 2, 2, 2, 1, 1, 1, 6, 17, 17, 17, 45, 65, 165, 165, 165, 165, 165, 1, 1, 19, 19, 19, 11, 11, 8, 8, 2, 6, 6, 17, 45, 45, 165, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 8, 9, 10, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
total number of confs: 434
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051806 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051806
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051806/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051806
Building REAL300025051807
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051807'
/scratch/stefan/7786831/working/building/REAL300025051807 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051807

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051807/0 /scratch/stefan/7786831/working/building/REAL300025051807 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 691)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/691
`/scratch/stefan/7786831/working/3D/691' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CC=CN=C2)CC1)

`REAL300025051807.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051807.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051807/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051807 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CC=CN=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 14, 48, 58, 104, 104, 104, 104, 104, 4, 1, 1, 1, 3, 3, 3, 9, 18, 18, 18, 18, 18, 1, 1, 48, 48, 104, 14, 4, 4, 3, 9, 9, 18, 18, 18, 18, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 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: REAL300025051807 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CC=CN=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 28, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 96, 104, 104, 104, 104, 146, 201, 201, 201, 201, 201, 104, 104, 28, 28, 1, 65, 96, 96, 104, 146, 146, 201, 201, 201, 201, 104, 104, 104, 104] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 721
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051807 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CC=CN=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 145, 161, 201, 201, 201, 201, 201, 26, 18, 12, 12, 6, 12, 1, 1, 1, 1, 1, 1, 1, 18, 18, 145, 145, 201, 69, 26, 26, 12, 6, 6, 1, 1, 1, 1, 18, 18, 18, 18] 201
rigid atoms, others: [34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 690
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051807 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051807
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051807/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051807
Building REAL300025051808
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051808'
/scratch/stefan/7786831/working/building/REAL300025051808 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051808

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051808/0 /scratch/stefan/7786831/working/building/REAL300025051808 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 692)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/692
`/scratch/stefan/7786831/working/3D/692' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1)

`REAL300025051808.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051808.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051808/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051808 none CCC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 6, 14, 14, 14, 51, 68, 139, 139, 139, 139, 139, 1, 1, 3, 8, 8, 8, 8, 8, 3, 3, 2, 6, 6, 14, 51, 51, 139, 1, 1, 1, 1] 201
rigid atoms, others: [39, 8, 9, 10, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 362
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051808 none CCC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 7, 15, 15, 15, 52, 69, 139, 139, 139, 139, 139, 3, 3, 1, 6, 6, 6, 5, 5, 1, 1, 3, 7, 7, 15, 52, 52, 139, 3, 3, 3, 3] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 24, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 358
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051808 none CCC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 139, 139, 139, 139, 139, 139, 139, 139, 99, 54, 54, 27, 54, 13, 1, 1, 1, 1, 1, 1, 1, 139, 139, 139, 201, 201, 201, 201, 201, 139, 139, 139, 99, 99, 54, 27, 27, 1, 139, 139, 139, 139] 201
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42])
total number of confs: 919
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051808 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051808
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051808/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051808
Building REAL300025051809
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051809'
/scratch/stefan/7786831/working/building/REAL300025051809 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051809

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051809/0 /scratch/stefan/7786831/working/building/REAL300025051809 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 693)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/693
`/scratch/stefan/7786831/working/3D/693' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051809.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051809.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051809/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051809 none NC(=O)C1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 6, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
177  conformations in input
total number of sets (complete confs): 177
using faster count positions algorithm for large data
unique positions, atoms: [8, 5, 8, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 5, 20, 20, 20, 54, 67, 112, 112, 112, 112, 112, 1, 1, 5, 8, 8, 5, 5, 5, 2, 5, 5, 20, 54, 54, 112, 1, 1, 1, 1, 5] 177
rigid atoms, others: [39, 40, 41, 10, 11, 12, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43])
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: REAL300025051809 none NC(=O)C1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 6, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
177  conformations in input
total number of sets (complete confs): 177
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 53, 53, 53, 107, 126, 170, 170, 170, 170, 170, 5, 5, 1, 3, 3, 1, 1, 1, 5, 13, 13, 53, 107, 107, 170, 5, 5, 5, 5, 1] 177
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 43, 26, 29, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 528
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051809 none NC(=O)C1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 6, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
177  conformations in input
total number of sets (complete confs): 177
using faster count positions algorithm for large data
unique positions, atoms: [177, 170, 177, 170, 170, 170, 170, 112, 112, 112, 112, 90, 60, 60, 29, 60, 13, 1, 1, 1, 1, 1, 1, 1, 112, 112, 170, 177, 177, 170, 170, 170, 112, 90, 90, 60, 29, 29, 1, 112, 112, 112, 112, 170] 177
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42, 43])
total number of confs: 546
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051809 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051809
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051809/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051809
Building REAL300025051810
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051810'
/scratch/stefan/7786831/working/building/REAL300025051810 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051810

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051810/0 /scratch/stefan/7786831/working/building/REAL300025051810 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 694)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/694
`/scratch/stefan/7786831/working/3D/694' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1=O)

`REAL300025051810.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051810.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051810/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051810 none CN1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 10, 2, 2, 2, 1, 1, 1, 7, 19, 19, 19, 46, 59, 132, 132, 132, 132, 132, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 7, 7, 19, 46, 46, 132, 1, 1, 1, 1, 10, 10] 201
rigid atoms, others: [7, 8, 9, 42, 43, 44, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 45, 46])
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: REAL300025051810 none CN1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 29, 50, 50, 50, 104, 121, 201, 201, 201, 201, 201, 10, 10, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 10, 29, 29, 50, 104, 104, 201, 10, 10, 10, 10, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 45, 46, 23, 24, 25, 33, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 601
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051810 none CN1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 132, 132, 132, 132, 100, 54, 54, 26, 54, 13, 1, 1, 1, 1, 1, 1, 1, 132, 132, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 132, 100, 100, 54, 26, 26, 1, 132, 132, 132, 132, 201, 201] 201
rigid atoms, others: [40, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46])
total number of confs: 727
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051810 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051810
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051810/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051810
Building REAL300025051811
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051811'
/scratch/stefan/7786831/working/building/REAL300025051811 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051811

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051811/0 /scratch/stefan/7786831/working/building/REAL300025051811 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 695)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/695
`/scratch/stefan/7786831/working/3D/695' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC1=O)

`REAL300025051811.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051811.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051811/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051811 none CN1C=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 19, 19, 19, 67, 79, 121, 121, 121, 121, 121, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 19, 67, 67, 121, 1, 1, 1, 1, 5] 201
rigid atoms, others: [38, 7, 8, 9, 39, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 42])
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: REAL300025051811 none CN1C=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 63, 63, 63, 133, 157, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 2, 2, 2, 1, 1, 5, 13, 13, 63, 133, 133, 201, 5, 5, 5, 5, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 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])
total number of confs: 643
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051811 none CN1C=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 121, 121, 121, 101, 60, 60, 26, 60, 13, 1, 1, 1, 1, 1, 1, 1, 121, 121, 201, 201, 201, 201, 201, 201, 201, 201, 121, 101, 101, 60, 26, 26, 1, 121, 121, 121, 121, 201] 201
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 591
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051811 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051811
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051811/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051811
Building REAL300025051812
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051812'
/scratch/stefan/7786831/working/building/REAL300025051812 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051812

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051812/0 /scratch/stefan/7786831/working/building/REAL300025051812 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 696)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/696
`/scratch/stefan/7786831/working/3D/696' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NCC(=O)NCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051812.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051812.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051812/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051812 none CC(=O)NCC(=O)NCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [188, 188, 188, 185, 134, 134, 134, 88, 86, 86, 86, 86, 68, 30, 30, 25, 30, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 188, 188, 188, 188, 185, 185, 134, 88, 88, 86, 68, 68, 30, 25, 25, 1, 86, 86, 86, 86] 188
rigid atoms, others: [42, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46])
total number of confs: 796
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: REAL300025051812 none CC(=O)NCC(=O)NCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [40, 40, 42, 36, 10, 10, 10, 3, 2, 2, 2, 1, 1, 1, 4, 17, 17, 17, 28, 31, 86, 86, 86, 86, 86, 1, 1, 42, 42, 42, 42, 36, 36, 10, 3, 3, 2, 4, 4, 17, 28, 28, 86, 1, 1, 1, 1] 188
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 345
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051812 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051812
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051812/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051812
Building REAL300025051813
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051813'
/scratch/stefan/7786831/working/building/REAL300025051813 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051813

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051813/0 /scratch/stefan/7786831/working/building/REAL300025051813 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 697)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/697
`/scratch/stefan/7786831/working/3D/697' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(F)(F)CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051813.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051813.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051813/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051813 none CC(F)(F)CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 15, 15, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 200, 158, 158, 158, 158, 135, 73, 73, 31, 73, 13, 1, 1, 1, 1, 1, 1, 1, 158, 158, 201, 201, 201, 201, 201, 200, 200, 158, 135, 135, 73, 31, 31, 1, 158, 158, 158, 158] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41])
total number of confs: 825
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051813 none CC(F)(F)CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 15, 15, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 13, 19, 19, 9, 2, 2, 2, 1, 1, 1, 6, 11, 11, 11, 36, 64, 158, 158, 158, 158, 158, 1, 1, 19, 19, 19, 13, 13, 9, 9, 2, 6, 6, 11, 36, 36, 158, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 8, 9, 10, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
total number of confs: 407
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051813 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051813
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051813/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051813
Building REAL300025051814
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051814'
/scratch/stefan/7786831/working/building/REAL300025051814 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051814

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051814/0 /scratch/stefan/7786831/working/building/REAL300025051814 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 698)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/698
`/scratch/stefan/7786831/working/3D/698' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(COC1CCCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051814.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051814.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051814/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051814 none O=C(COC1CCCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 5, 11, 21, 21, 21, 21, 21, 1, 1, 1, 4, 11, 11, 11, 32, 43, 104, 104, 104, 104, 104, 1, 1, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 4, 4, 11, 32, 32, 104, 1, 1, 1, 1] 201
rigid atoms, others: [10, 11, 12, 46, 47, 48, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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: REAL300025051814 none O=C(COC1CCCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 11, 5, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 46, 71, 71, 71, 121, 142, 201, 201, 201, 201, 201, 22, 22, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 46, 46, 71, 121, 121, 201, 22, 22, 22, 22] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 37, 35, 36, 38, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 663
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051814 none O=C(COC1CCCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [103, 103, 103, 125, 183, 201, 201, 201, 201, 201, 103, 84, 63, 63, 47, 63, 13, 1, 1, 1, 1, 1, 1, 1, 103, 103, 125, 125, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 103, 84, 84, 63, 47, 47, 1, 103, 103, 103, 103] 201
rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49])
total number of confs: 703
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051814 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051814
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051814/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051814
Building REAL300025051815
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051815'
/scratch/stefan/7786831/working/building/REAL300025051815 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051815

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051815/0 /scratch/stefan/7786831/working/building/REAL300025051815 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 699)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/699
`/scratch/stefan/7786831/working/3D/699' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCOCC(F)(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051815.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051815.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051815/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051815 none O=C(CCOCC(F)(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 15, 15, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [99, 99, 99, 190, 190, 194, 201, 201, 201, 201, 99, 83, 64, 64, 30, 64, 13, 1, 1, 1, 1, 1, 1, 1, 99, 99, 190, 190, 190, 190, 201, 201, 99, 83, 83, 64, 30, 30, 1, 99, 99, 99, 99] 201
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42])
total number of confs: 828
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051815 none O=C(CCOCC(F)(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 15, 15, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 10, 10, 21, 37, 37, 37, 37, 1, 1, 1, 3, 5, 5, 5, 18, 31, 99, 99, 99, 99, 99, 1, 1, 10, 10, 10, 10, 37, 37, 2, 3, 3, 5, 18, 18, 99, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 10, 11, 12, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 317
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051815 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051815
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051815/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051815
Building REAL300025051816
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051816'
/scratch/stefan/7786831/working/building/REAL300025051816 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051816

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051816/0 /scratch/stefan/7786831/working/building/REAL300025051816 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 700)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/700
`/scratch/stefan/7786831/working/3D/700' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCOCC1CCCO1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051816.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051816.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051816/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051816 none O=C(CCOCC1CCCO1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 5, 5, 12, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 8, 8, 14, 25, 39, 39, 39, 39, 1, 1, 1, 4, 6, 6, 6, 21, 34, 94, 94, 94, 94, 94, 1, 1, 8, 8, 8, 8, 25, 25, 39, 39, 39, 39, 39, 39, 39, 2, 4, 4, 6, 21, 21, 94, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 47, 48, 49, 50, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 317
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051816 none O=C(CCOCC1CCCO1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 5, 5, 12, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [39, 25, 20, 12, 5, 1, 1, 1, 1, 1, 1, 39, 39, 39, 47, 56, 56, 56, 106, 141, 201, 201, 201, 201, 201, 39, 39, 25, 25, 20, 20, 5, 5, 1, 1, 1, 1, 1, 1, 1, 39, 47, 47, 56, 106, 106, 201, 39, 39, 39, 39] 201
rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 39, 38, 37] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 649
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051816 none O=C(CCOCC1CCCO1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 5, 5, 12, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [94, 94, 94, 138, 138, 181, 191, 201, 201, 201, 201, 94, 89, 64, 64, 30, 64, 13, 1, 1, 1, 1, 1, 1, 1, 94, 94, 138, 138, 138, 138, 191, 191, 201, 201, 201, 201, 201, 201, 201, 94, 89, 89, 64, 30, 30, 1, 94, 94, 94, 94] 201
rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50])
total number of confs: 726
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051816 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051816
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051816/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051816
Building REAL300025051817
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051817'
/scratch/stefan/7786831/working/building/REAL300025051817 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051817

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051817/0 /scratch/stefan/7786831/working/building/REAL300025051817 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 701)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/701
`/scratch/stefan/7786831/working/3D/701' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CC=NC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051817.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051817.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051817/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051817 none O=C(CCC1=CC=NC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 8, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 9, 12, 12, 12, 12, 12, 12, 1, 1, 1, 7, 18, 18, 18, 47, 68, 160, 160, 160, 160, 160, 1, 1, 9, 9, 12, 12, 12, 12, 12, 12, 2, 7, 7, 18, 47, 47, 160, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 10, 11, 12, 44, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 400
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051817 none O=C(CCC1=CC=NC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 8, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 4, 2, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 34, 53, 53, 53, 103, 130, 201, 201, 201, 201, 201, 12, 12, 4, 4, 2, 2, 1, 1, 1, 1, 12, 34, 34, 53, 103, 103, 201, 12, 12, 12, 12] 201
rigid atoms, others: [32, 33, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 611
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051817 none O=C(CCC1=CC=NC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 8, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [160, 160, 160, 199, 201, 201, 201, 201, 201, 201, 160, 123, 54, 54, 30, 54, 13, 1, 1, 1, 1, 1, 1, 1, 160, 160, 199, 199, 201, 201, 201, 201, 201, 201, 160, 123, 123, 54, 30, 30, 1, 160, 160, 160, 160] 201
rigid atoms, others: [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, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 861
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051817 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051817
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051817/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051817
Building REAL300025051818
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051818'
/scratch/stefan/7786831/working/building/REAL300025051818 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051818

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051818/0 /scratch/stefan/7786831/working/building/REAL300025051818 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 702)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/702
`/scratch/stefan/7786831/working/3D/702' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)N1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1)

`REAL300025051818.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051818.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051818/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051818 none CC(C)(C)N1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 5, 9, 9, 5, 5, 2, 2, 2, 1, 1, 1, 4, 20, 20, 20, 58, 71, 153, 153, 153, 153, 153, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 2, 4, 4, 20, 58, 58, 153, 1, 1, 1, 1, 5] 201
rigid atoms, others: [9, 10, 11, 44, 45, 46, 47, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48])
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: REAL300025051818 none CC(C)(C)N1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 5, 5, 5, 5, 12, 41, 41, 41, 101, 119, 201, 201, 201, 201, 201, 5, 5, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 5, 12, 12, 41, 101, 101, 201, 5, 5, 5, 5, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 48, 25, 36, 26] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 562
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051818 none CC(C)(C)N1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 153, 153, 153, 153, 132, 84, 84, 37, 84, 13, 1, 1, 1, 1, 1, 1, 1, 153, 153, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 153, 132, 132, 84, 37, 37, 1, 153, 153, 153, 153, 201] 201
rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48])
total number of confs: 656
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051818 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051818
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051818/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051818
Building REAL300025051819
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051819'
/scratch/stefan/7786831/working/building/REAL300025051819 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051819

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051819/0 /scratch/stefan/7786831/working/building/REAL300025051819 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 703)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/703
`/scratch/stefan/7786831/working/3D/703' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC(=O)NC2)CC1)

`REAL300025051819.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051819.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051819/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051819 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC(=O)NC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 26, 26, 73, 85, 158, 158, 158, 158, 158, 5, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 13, 1, 1, 73, 73, 158, 26, 5, 5, 3, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 428
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051819 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC(=O)NC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [72, 32, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 127, 158, 158, 158, 158, 201, 201, 201, 201, 201, 201, 158, 158, 32, 32, 1, 72, 127, 127, 158, 201, 201, 201, 201, 201, 201, 201, 201, 158, 158, 158, 158] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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])
total number of confs: 714
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051819 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC(=O)NC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [77, 77, 77, 147, 157, 201, 201, 201, 201, 201, 20, 13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 13, 13, 147, 147, 201, 77, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42, 43])
total number of confs: 663
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051819 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051819
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051819/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051819
Building REAL300025051820
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051820'
/scratch/stefan/7786831/working/building/REAL300025051820 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051820

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051820/0 /scratch/stefan/7786831/working/building/REAL300025051820 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 704)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/704
`/scratch/stefan/7786831/working/3D/704' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=N1)

`REAL300025051820.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051820.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051820/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051820 none COC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 19, 19, 19, 64, 75, 117, 117, 117, 117, 117, 1, 1, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 19, 64, 64, 117, 1, 1, 1, 1, 5, 5] 201
rigid atoms, others: [37, 38, 7, 8, 9, 39, 40, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 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, 41, 42])
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: REAL300025051820 none COC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 61, 61, 61, 145, 162, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 2, 2, 2, 1, 5, 13, 13, 61, 145, 145, 201, 5, 5, 5, 5, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 42, 23, 24, 25, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 672
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051820 none COC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 117, 117, 117, 117, 95, 61, 61, 26, 61, 13, 1, 1, 1, 1, 1, 1, 1, 117, 117, 201, 201, 201, 201, 201, 201, 201, 117, 95, 95, 61, 26, 26, 1, 117, 117, 117, 117, 201, 201] 201
rigid atoms, others: [36, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42])
total number of confs: 564
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051820 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051820
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051820/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051820
Building REAL300025051821
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051821'
/scratch/stefan/7786831/working/building/REAL300025051821 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051821

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051821/0 /scratch/stefan/7786831/working/building/REAL300025051821 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 705)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/705
`/scratch/stefan/7786831/working/3D/705' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1)

`REAL300025051821.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051821.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051821/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051821 none CN(C)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)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.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
195  conformations in input
total number of sets (complete confs): 195
using faster count positions algorithm for large data
unique positions, atoms: [13, 5, 13, 5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 14, 14, 14, 43, 57, 160, 160, 160, 160, 160, 1, 1, 5, 5, 13, 13, 13, 13, 13, 13, 5, 5, 2, 4, 4, 14, 43, 43, 160, 1, 1, 1, 1, 5] 195
rigid atoms, others: [43, 9, 10, 11, 44, 45, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46])
total number of confs: 363
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051821 none CN(C)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)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.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 27, 27, 27, 66, 82, 195, 195, 195, 195, 195, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 5, 12, 12, 27, 66, 66, 195, 5, 5, 5, 5, 1] 195
rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 7, 46, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 478
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051821 none CN(C)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)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.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 160, 160, 160, 160, 136, 86, 86, 35, 86, 13, 1, 1, 1, 1, 1, 1, 1, 160, 160, 195, 195, 195, 195, 195, 195, 195, 195, 195, 195, 160, 136, 136, 86, 35, 35, 1, 160, 160, 160, 160, 195] 195
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46])
total number of confs: 670
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051821 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051821
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051821/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051821
Building REAL300025051822
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051822'
/scratch/stefan/7786831/working/building/REAL300025051822 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051822

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051822/0 /scratch/stefan/7786831/working/building/REAL300025051822 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 706)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/706
`/scratch/stefan/7786831/working/3D/706' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051822.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051822.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051822/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051822 none CC(C)(C)C1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 4, 7, 7, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 23, 23, 23, 68, 77, 196, 196, 196, 196, 196, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 2, 7, 7, 23, 68, 68, 196, 1, 1, 1, 1, 4] 201
rigid atoms, others: [44, 10, 11, 12, 45, 46, 47, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48])
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: REAL300025051822 none CC(C)(C)C1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 28, 28, 28, 75, 85, 201, 201, 201, 201, 201, 4, 4, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 11, 11, 28, 75, 75, 201, 4, 4, 4, 4, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 48, 36, 26] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 497
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051822 none CC(C)(C)C1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 196, 196, 196, 196, 126, 58, 58, 28, 58, 13, 1, 1, 1, 1, 1, 1, 1, 196, 196, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 196, 126, 126, 58, 28, 28, 1, 196, 196, 196, 196, 201] 201
rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48])
total number of confs: 720
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051822 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051822
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051822/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051822
Building REAL300025051823
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051823'
/scratch/stefan/7786831/working/building/REAL300025051823 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051823

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051823/0 /scratch/stefan/7786831/working/building/REAL300025051823 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 707)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/707
`/scratch/stefan/7786831/working/3D/707' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NNC3=C2CCC3)CC1)

`REAL300025051823.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051823.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051823/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051823 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NNC3=C2CCC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 31, 31, 107, 119, 201, 201, 201, 201, 201, 6, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 1, 1, 107, 107, 201, 31, 6, 6, 3, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 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: REAL300025051823 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NNC3=C2CCC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 31, 13, 1, 1, 1, 1, 1, 1, 1, 55, 55, 146, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 31, 31, 1, 55, 146, 146, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 761
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051823 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NNC3=C2CCC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [47, 47, 47, 130, 139, 201, 201, 201, 201, 201, 11, 6, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 130, 130, 201, 47, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43])
total number of confs: 621
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051823 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051823/1 /scratch/stefan/7786831/working/building/REAL300025051823 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 708)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/708
`/scratch/stefan/7786831/working/3D/708' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCCC3=NN2)CC1)

`REAL300025051823.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051823.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051823/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051823 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCCC3=NN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 107, 129, 196, 196, 196, 196, 196, 6, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 1, 1, 107, 107, 196, 28, 6, 6, 3, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 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: REAL300025051823 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCCC3=NN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 34, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 160, 196, 196, 196, 196, 201, 201, 201, 201, 201, 201, 201, 196, 196, 34, 34, 1, 84, 160, 160, 196, 201, 201, 201, 201, 201, 201, 201, 196, 196, 196, 196] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 736
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051823 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCCC3=NN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 149, 159, 201, 201, 201, 201, 201, 17, 9, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 149, 149, 201, 59, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43])
total number of confs: 667
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051823 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051823
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051823/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051823/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051823
Building REAL300025051824
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051824'
/scratch/stefan/7786831/working/building/REAL300025051824 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051824

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051824/0 /scratch/stefan/7786831/working/building/REAL300025051824 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 709)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/709
`/scratch/stefan/7786831/working/3D/709' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NNC3=C2CCCC3)CC1)

`REAL300025051824.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051824.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051824/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051824 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NNC3=C2CCCC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 30, 98, 111, 201, 201, 201, 201, 201, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 98, 98, 201, 30, 6, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 532
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051824 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NNC3=C2CCCC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 31, 13, 1, 1, 1, 1, 1, 1, 1, 57, 57, 144, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 31, 31, 1, 57, 144, 144, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46])
total number of confs: 748
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051824 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NNC3=C2CCCC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 48, 134, 142, 201, 201, 201, 201, 201, 12, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 134, 134, 201, 48, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46])
total number of confs: 630
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051824 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051824/1 /scratch/stefan/7786831/working/building/REAL300025051824 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 710)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/710
`/scratch/stefan/7786831/working/3D/710' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCCCC3=NN2)CC1)

`REAL300025051824.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051824.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051824/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051824 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCCCC3=NN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [28, 28, 28, 88, 107, 178, 178, 178, 178, 178, 6, 1, 1, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 88, 88, 178, 28, 6, 6, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1] 199
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 501
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: REAL300025051824 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCCCC3=NN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [87, 38, 13, 1, 1, 1, 1, 1, 1, 1, 87, 87, 145, 178, 178, 178, 178, 199, 199, 199, 199, 199, 199, 199, 199, 178, 178, 38, 38, 1, 87, 145, 145, 178, 199, 199, 199, 199, 199, 199, 199, 199, 199, 178, 178, 178, 178] 199
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46])
total number of confs: 689
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051824 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCCCC3=NN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [69, 69, 69, 139, 155, 199, 199, 199, 199, 199, 26, 17, 10, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 139, 139, 199, 69, 26, 26, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17] 199
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46])
total number of confs: 655
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051824 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051824
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051824/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051824/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051824
Building REAL300025051825
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051825'
/scratch/stefan/7786831/working/building/REAL300025051825 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051825

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051825/0 /scratch/stefan/7786831/working/building/REAL300025051825 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 711)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/711
`/scratch/stefan/7786831/working/3D/711' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NNN=C2)CC1)

`REAL300025051825.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051825.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051825/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051825 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NNN=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 8, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 31, 31, 109, 121, 201, 201, 201, 201, 201, 6, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 1, 1, 109, 109, 201, 31, 6, 6, 3, 5, 5, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 563
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051825 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NNN=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 8, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [64, 32, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 152, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 32, 32, 1, 64, 152, 152, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 25] set([0, 1, 2, 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])
total number of confs: 742
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051825 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NNN=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 8, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [41, 41, 41, 115, 127, 201, 201, 201, 201, 201, 9, 5, 4, 3, 1, 3, 1, 1, 1, 1, 1, 5, 5, 115, 115, 201, 41, 9, 9, 4, 1, 1, 5, 5, 5, 5] 201
rigid atoms, others: [14, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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
/scratch/stefan/7786831/working/building/REAL300025051825 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051825/1 /scratch/stefan/7786831/working/building/REAL300025051825 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 712)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/712
`/scratch/stefan/7786831/working/3D/712' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=NN2)CC1)

`REAL300025051825.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051825.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051825/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051825 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=NN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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: [11, 11, 11, 33, 51, 93, 93, 93, 93, 93, 5, 1, 1, 1, 3, 3, 3, 16, 16, 16, 16, 1, 1, 33, 33, 93, 11, 5, 5, 3, 16, 16, 1, 1, 1, 1] 114
rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 247
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051825 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=NN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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: [63, 43, 13, 1, 1, 1, 1, 1, 1, 1, 63, 63, 87, 93, 94, 94, 94, 114, 114, 114, 114, 93, 93, 43, 43, 1, 63, 87, 87, 94, 114, 114, 93, 93, 93, 93] 114
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 25] set([0, 1, 2, 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])
total number of confs: 407
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051825 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=NN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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: [33, 33, 33, 57, 76, 114, 114, 114, 114, 114, 23, 16, 10, 10, 1, 10, 1, 1, 1, 1, 1, 16, 16, 57, 57, 114, 33, 23, 23, 10, 1, 1, 16, 16, 16, 16] 114
rigid atoms, others: [14, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35])
total number of confs: 328
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051825 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051825
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051825/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051825/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051825
Building REAL300025051826
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051826'
/scratch/stefan/7786831/working/building/REAL300025051826 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051826

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051826/0 /scratch/stefan/7786831/working/building/REAL300025051826 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 713)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/713
`/scratch/stefan/7786831/working/3D/713' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NN1C)

`REAL300025051826.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051826.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051826/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051826 none CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 28, 28, 28, 97, 123, 201, 201, 201, 201, 201, 1, 1, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 28, 97, 97, 201, 1, 1, 1, 1, 4, 4, 4] 201
rigid atoms, others: [36, 37, 6, 7, 8, 39, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 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, 40, 41, 42])
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: REAL300025051826 none CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 4, 4, 11, 35, 35, 35, 103, 128, 201, 201, 201, 201, 201, 4, 4, 1, 1, 1, 2, 2, 2, 1, 4, 11, 11, 35, 103, 103, 201, 4, 4, 4, 4, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 22, 23, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 585
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051826 none CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 135, 60, 60, 30, 60, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 135, 135, 60, 30, 30, 1, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 766
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051826 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051826
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051826/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051826
Building REAL300025051827
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051827'
/scratch/stefan/7786831/working/building/REAL300025051827 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051827

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051827/0 /scratch/stefan/7786831/working/building/REAL300025051827 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 714)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/714
`/scratch/stefan/7786831/working/3D/714' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CN=N1)

`REAL300025051827.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051827.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051827/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051827 none CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CN=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.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, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
192  conformations in input
total number of sets (complete confs): 192
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 20, 20, 20, 67, 83, 139, 139, 139, 139, 139, 1, 1, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 20, 67, 67, 139, 1, 1, 1, 1, 5] 192
rigid atoms, others: [36, 37, 6, 7, 8, 39, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 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, 40])
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: REAL300025051827 none CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CN=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.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, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
192  conformations in input
total number of sets (complete confs): 192
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 56, 56, 56, 127, 150, 192, 192, 192, 192, 192, 5, 5, 1, 1, 1, 2, 2, 2, 1, 5, 13, 13, 56, 127, 127, 192, 5, 5, 5, 5, 1] 192
rigid atoms, others: [0, 1, 2, 3, 4, 40, 22, 23, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 610
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051827 none CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CN=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.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, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
192  conformations in input
total number of sets (complete confs): 192
using faster count positions algorithm for large data
unique positions, atoms: [192, 192, 192, 139, 139, 139, 139, 115, 77, 77, 32, 77, 13, 1, 1, 1, 1, 1, 1, 1, 139, 139, 192, 192, 192, 192, 192, 192, 192, 139, 115, 115, 77, 32, 32, 1, 139, 139, 139, 139, 192] 192
rigid atoms, others: [35, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40])
total number of confs: 602
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051827 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051827
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051827/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051827
Building REAL300025051828
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051828'
/scratch/stefan/7786831/working/building/REAL300025051828 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051828

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051828/0 /scratch/stefan/7786831/working/building/REAL300025051828 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 715)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/715
`/scratch/stefan/7786831/working/3D/715' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C[NH+]2CCC(CO)CC2)CC1)

`REAL300025051828.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051828.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051828/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051828 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C[NH+]2CCC(CO)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 13, 17, 29, 29, 29, 29, 29, 4, 1, 1, 1, 3, 3, 3, 4, 8, 8, 8, 8, 8, 13, 8, 8, 1, 1, 13, 13, 29, 6, 4, 4, 3, 4, 4, 8, 8, 8, 8, 8, 13, 13, 39, 8, 8, 8, 8, 1, 1, 1, 1] 93
rigid atoms, others: [11, 12, 13, 49, 50, 51, 52, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
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: REAL300025051828 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C[NH+]2CCC(CO)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [26, 20, 10, 1, 1, 1, 1, 1, 1, 1, 26, 26, 28, 29, 29, 29, 29, 31, 31, 31, 31, 31, 31, 31, 31, 31, 29, 29, 20, 20, 1, 26, 28, 28, 29, 31, 31, 31, 31, 31, 31, 31, 31, 31, 93, 31, 31, 31, 31, 29, 29, 29, 29] 93
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 208
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051828 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C[NH+]2CCC(CO)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 19, 22, 31, 31, 31, 31, 31, 9, 8, 8, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 6, 1, 1, 8, 8, 19, 19, 31, 11, 9, 9, 8, 5, 5, 1, 1, 1, 1, 1, 6, 6, 18, 1, 1, 1, 1, 8, 8, 8, 8] 93
rigid atoms, others: [48, 37, 38, 39, 40, 41, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 49, 50, 51, 52])
total number of confs: 139
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051828 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051828/1 /scratch/stefan/7786831/working/building/REAL300025051828 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 716)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/716
`/scratch/stefan/7786831/working/3D/716' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2CCC(CO)CC2)CC1)

`REAL300025051828.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051828.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051828/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051828 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2CCC(CO)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 12, 41, 55, 157, 157, 157, 157, 157, 4, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 12, 6, 6, 1, 1, 41, 41, 157, 12, 4, 4, 3, 6, 6, 6, 6, 6, 6, 6, 12, 12, 36, 6, 6, 6, 6, 1, 1, 1, 1] 603
rigid atoms, others: [11, 12, 13, 48, 49, 50, 51, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 405
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051828 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2CCC(CO)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [65, 32, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 141, 157, 157, 157, 157, 201, 201, 201, 201, 201, 201, 201, 201, 157, 157, 32, 32, 1, 65, 141, 141, 157, 201, 201, 201, 201, 201, 201, 201, 201, 201, 603, 201, 201, 201, 201, 157, 157, 157, 157] 603
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 1454
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051828 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2CCC(CO)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 25, 76, 96, 201, 201, 201, 201, 201, 9, 6, 4, 4, 3, 4, 1, 1, 1, 1, 1, 1, 5, 1, 1, 6, 6, 76, 76, 201, 25, 9, 9, 4, 3, 3, 1, 1, 1, 1, 1, 5, 5, 15, 1, 1, 1, 1, 6, 6, 6, 6] 603
rigid atoms, others: [36, 37, 38, 39, 40, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 48, 49, 50, 51])
total number of confs: 533
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051828 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051828
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051828/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051828/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051828
Building REAL300025051829
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051829'
/scratch/stefan/7786831/working/building/REAL300025051829 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051829

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051829/0 /scratch/stefan/7786831/working/building/REAL300025051829 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 717)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/717
`/scratch/stefan/7786831/working/3D/717' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC=C2O)CC1)

`REAL300025051829.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051829.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051829/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051829 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC=C2O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 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]
1  hydrogens need rotated
262  conformations in input
total number of sets (complete confs): 262
using faster count positions algorithm for large data
unique positions, atoms: [23, 23, 23, 67, 82, 118, 118, 118, 118, 118, 5, 1, 1, 1, 3, 3, 3, 8, 8, 5, 8, 8, 8, 1, 1, 67, 67, 118, 23, 5, 5, 3, 8, 8, 8, 8, 16, 1, 1, 1, 1] 262
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 379
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: REAL300025051829 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC=C2O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 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]
1  hydrogens need rotated
262  conformations in input
total number of sets (complete confs): 262
using faster count positions algorithm for large data
unique positions, atoms: [61, 27, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 100, 118, 118, 118, 118, 131, 131, 131, 131, 131, 131, 118, 118, 27, 27, 1, 61, 100, 100, 118, 131, 131, 131, 131, 262, 118, 118, 118, 118] 262
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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])
total number of confs: 735
number of broken/clashed sets: 52
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051829 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC=C2O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 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]
1  hydrogens need rotated
262  conformations in input
total number of sets (complete confs): 262
using faster count positions algorithm for large data
unique positions, atoms: [49, 49, 49, 100, 110, 131, 131, 131, 131, 131, 14, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 100, 100, 131, 49, 14, 14, 5, 1, 1, 1, 1, 2, 8, 8, 8, 8] 262
rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40])
total number of confs: 441
number of broken/clashed sets: 52
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051829 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051829
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051829/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051829
Building REAL300025051830
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051830'
/scratch/stefan/7786831/working/building/REAL300025051830 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051830

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051830/0 /scratch/stefan/7786831/working/building/REAL300025051830 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 718)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/718
`/scratch/stefan/7786831/working/3D/718' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=C1Cl)

`REAL300025051830.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051830.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051830/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051830 none NC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 16, 6, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 2, 2, 1, 1, 1, 4, 19, 19, 19, 53, 60, 102, 102, 102, 102, 102, 1, 1, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 19, 53, 53, 102, 1, 1, 1, 1, 5, 5] 201
rigid atoms, others: [36, 37, 6, 7, 8, 39, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 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, 40, 41])
total number of confs: 291
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051830 none NC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 16, 6, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 5, 5, 5, 5, 13, 64, 64, 64, 135, 153, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 1, 2, 2, 1, 5, 13, 13, 64, 135, 135, 201, 5, 5, 5, 5, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 40, 41, 22, 23, 24, 25, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 645
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051830 none NC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 16, 6, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 102, 102, 102, 102, 84, 54, 54, 25, 54, 13, 1, 1, 1, 1, 1, 1, 1, 102, 102, 201, 201, 201, 201, 201, 201, 201, 102, 84, 84, 54, 25, 25, 1, 102, 102, 102, 102, 201, 201] 201
rigid atoms, others: [35, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41])
total number of confs: 537
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051830 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051830
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051830/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051830
Building REAL300025051831
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051831'
/scratch/stefan/7786831/working/building/REAL300025051831 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051831

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051831/0 /scratch/stefan/7786831/working/building/REAL300025051831 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 719)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/719
`/scratch/stefan/7786831/working/3D/719' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CSC2=CC=NC=C2)CC1)

`REAL300025051831.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051831.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051831/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051831 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CSC2=CC=NC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 1, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 39, 42, 75, 75, 75, 75, 75, 5, 1, 1, 1, 3, 3, 3, 16, 42, 56, 56, 53, 56, 56, 1, 1, 39, 39, 75, 17, 5, 5, 3, 16, 16, 56, 56, 56, 56, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 322
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: REAL300025051831 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CSC2=CC=NC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 1, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [44, 26, 13, 1, 1, 1, 1, 1, 1, 1, 44, 44, 67, 75, 75, 75, 75, 134, 197, 201, 201, 201, 201, 201, 75, 75, 26, 26, 1, 44, 67, 67, 75, 134, 134, 201, 201, 201, 201, 75, 75, 75, 75] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 643
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051831 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CSC2=CC=NC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 1, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [136, 136, 136, 194, 194, 201, 201, 201, 201, 201, 74, 56, 53, 53, 20, 53, 5, 1, 1, 1, 1, 1, 1, 1, 56, 56, 194, 194, 201, 136, 74, 74, 53, 20, 20, 1, 1, 1, 1, 56, 56, 56, 56] 201
rigid atoms, others: [35, 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, 39, 40, 41, 42])
total number of confs: 809
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051831 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051831
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051831/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051831
Building REAL300025051832
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051832'
/scratch/stefan/7786831/working/building/REAL300025051832 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051832

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051832/0 /scratch/stefan/7786831/working/building/REAL300025051832 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 720)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/720
`/scratch/stefan/7786831/working/3D/720' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1O)

`REAL300025051832.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051832.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051832/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051832 none CC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 3, 5, 5, 2, 2, 2, 1, 1, 1, 5, 23, 23, 23, 65, 76, 167, 168, 168, 168, 168, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 2, 5, 5, 23, 65, 65, 168, 1, 1, 1, 1, 10] 402
rigid atoms, others: [39, 8, 9, 10, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 43])
total number of confs: 417
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051832 none CC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 12, 54, 54, 54, 128, 137, 199, 201, 201, 201, 201, 5, 5, 1, 1, 2, 2, 2, 1, 1, 1, 5, 12, 12, 54, 128, 128, 201, 5, 5, 5, 5, 2] 402
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 25, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 623
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051832 none CC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
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, 168, 168, 168, 168, 121, 57, 57, 28, 57, 13, 1, 1, 1, 1, 1, 1, 1, 168, 168, 201, 201, 201, 201, 201, 201, 201, 201, 168, 121, 121, 57, 28, 28, 1, 168, 168, 168, 168, 402] 402
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42, 43])
total number of confs: 1101
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051832 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051832
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051832/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051832
Building REAL300025051833
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051833'
/scratch/stefan/7786831/working/building/REAL300025051833 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051833

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051833/0 /scratch/stefan/7786831/working/building/REAL300025051833 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 721)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/721
`/scratch/stefan/7786831/working/3D/721' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3NC=NC3=C2)CC1)

`REAL300025051833.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051833.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051833/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051833 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3NC=NC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 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: [19, 19, 19, 65, 74, 150, 150, 150, 150, 150, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 65, 65, 150, 19, 5, 5, 3, 9, 9, 9, 9, 9, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 390
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051833 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3NC=NC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 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: [70, 35, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 121, 150, 150, 150, 150, 201, 201, 201, 201, 201, 201, 201, 201, 150, 150, 35, 35, 1, 70, 121, 121, 150, 201, 201, 201, 201, 201, 150, 150, 150, 150] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 642
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051833 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3NC=NC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 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: [54, 54, 54, 136, 145, 201, 201, 201, 201, 201, 16, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 136, 136, 201, 54, 16, 16, 5, 1, 1, 1, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42])
total number of confs: 649
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051833 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051833
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051833/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051833
Building REAL300025051834
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051834'
/scratch/stefan/7786831/working/building/REAL300025051834 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051834

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051834/0 /scratch/stefan/7786831/working/building/REAL300025051834 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 722)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/722
`/scratch/stefan/7786831/working/3D/722' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CSCCS2)CC1)

`REAL300025051834.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051834.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051834/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051834 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CSCCS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'S.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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 14, 5, 5, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 71, 79, 156, 156, 156, 156, 156, 5, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 1, 1, 71, 71, 156, 22, 5, 5, 3, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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: REAL300025051834 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CSCCS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'S.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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 14, 5, 5, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [68, 31, 13, 1, 1, 1, 1, 1, 1, 1, 68, 68, 127, 156, 156, 156, 156, 201, 201, 201, 201, 201, 156, 156, 31, 31, 1, 68, 127, 127, 156, 201, 201, 201, 201, 201, 201, 201, 156, 156, 156, 156] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 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: 735
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051834 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CSCCS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'S.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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 14, 5, 5, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [71, 71, 71, 152, 160, 201, 201, 201, 201, 201, 22, 14, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 152, 152, 201, 71, 22, 22, 8, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41])
total number of confs: 682
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051834 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051834
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051834/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051834
Building REAL300025051835
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051835'
/scratch/stefan/7786831/working/building/REAL300025051835 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051835

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051835/0 /scratch/stefan/7786831/working/building/REAL300025051835 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 723)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/723
`/scratch/stefan/7786831/working/3D/723' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(Cl)=CC=N2)CC1)

`REAL300025051835.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051835.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051835/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051835 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(Cl)=CC=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 32, 32, 100, 112, 199, 199, 199, 199, 199, 7, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 1, 1, 100, 100, 199, 32, 7, 7, 3, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 532
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051835 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(Cl)=CC=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [65, 33, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 143, 199, 199, 199, 199, 201, 201, 201, 201, 201, 201, 199, 199, 33, 33, 1, 65, 143, 143, 199, 201, 201, 201, 199, 199, 199, 199] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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])
total number of confs: 734
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051835 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(Cl)=CC=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [51, 51, 51, 126, 135, 201, 201, 201, 201, 201, 12, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 126, 126, 201, 51, 12, 12, 4, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38])
total number of confs: 598
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051835 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051835
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051835/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051835
Building REAL300025051836
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051836'
/scratch/stefan/7786831/working/building/REAL300025051836 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051836

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051836/0 /scratch/stefan/7786831/working/building/REAL300025051836 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 724)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/724
`/scratch/stefan/7786831/working/3D/724' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CO)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051836.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051836.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051836/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051836 none O=C(CO)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 193, 93, 93, 34, 93, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 603, 201, 193, 193, 93, 34, 34, 1, 201, 201, 201, 201] 603
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33])
total number of confs: 1366
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: REAL300025051836 none O=C(CO)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 6, 1, 1, 1, 7, 25, 25, 25, 96, 139, 201, 201, 201, 201, 201, 1, 1, 6, 6, 18, 2, 7, 7, 25, 96, 96, 201, 1, 1, 1, 1] 603
rigid atoms, others: [32, 33, 4, 5, 6, 18, 19, 30, 31] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 565
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051836 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051836
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051836/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051836
Building REAL300025051837
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051837'
/scratch/stefan/7786831/working/building/REAL300025051837 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051837

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051837/0 /scratch/stefan/7786831/working/building/REAL300025051837 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 725)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/725
`/scratch/stefan/7786831/working/3D/725' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC(O)=C2)CC1)

`REAL300025051837.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051837.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051837/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051837 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC(O)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 18, 59, 68, 124, 124, 124, 124, 124, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 1, 1, 59, 59, 124, 18, 5, 5, 3, 9, 9, 9, 18, 9, 1, 1, 1, 1] 402
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
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: REAL300025051837 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC(O)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [59, 31, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 103, 124, 124, 124, 124, 201, 201, 201, 201, 201, 201, 124, 124, 31, 31, 1, 59, 103, 103, 124, 201, 201, 201, 402, 201, 124, 124, 124, 124] 402
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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])
total number of confs: 991
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051837 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC(O)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [54, 54, 54, 141, 154, 201, 201, 201, 201, 201, 17, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 9, 9, 141, 141, 201, 54, 17, 17, 5, 1, 1, 1, 2, 1, 9, 9, 9, 9] 402
rigid atoms, others: [32, 33, 34, 36, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 37, 38, 39, 40])
total number of confs: 678
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051837 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051837
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051837/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051837
Building REAL300025051838
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051838'
/scratch/stefan/7786831/working/building/REAL300025051838 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051838

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051838/0 /scratch/stefan/7786831/working/building/REAL300025051838 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 726)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/726
`/scratch/stefan/7786831/working/3D/726' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(Cl)=CC=C2O)CC1)

`REAL300025051838.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051838.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051838/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051838 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(Cl)=CC=C2O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
256  conformations in input
total number of sets (complete confs): 256
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 69, 83, 118, 118, 118, 118, 118, 5, 1, 1, 1, 3, 3, 3, 10, 10, 10, 3, 10, 10, 10, 1, 1, 69, 69, 118, 24, 5, 5, 3, 10, 10, 10, 20, 1, 1, 1, 1] 256
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 395
number of broken/clashed sets: 56
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051838 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(Cl)=CC=C2O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
256  conformations in input
total number of sets (complete confs): 256
using faster count positions algorithm for large data
unique positions, atoms: [57, 26, 12, 1, 1, 1, 1, 1, 1, 1, 57, 57, 96, 118, 118, 118, 118, 128, 128, 128, 118, 128, 128, 128, 118, 118, 26, 26, 1, 57, 96, 96, 118, 128, 128, 128, 256, 118, 118, 118, 118] 256
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 769
number of broken/clashed sets: 56
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051838 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(Cl)=CC=C2O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
256  conformations in input
total number of sets (complete confs): 256
using faster count positions algorithm for large data
unique positions, atoms: [50, 50, 50, 100, 108, 128, 128, 128, 128, 128, 15, 10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 100, 100, 128, 50, 15, 15, 6, 1, 1, 1, 2, 10, 10, 10, 10] 256
rigid atoms, others: [33, 34, 35, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40])
total number of confs: 437
number of broken/clashed sets: 56
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051838 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051838/1 /scratch/stefan/7786831/working/building/REAL300025051838 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 727)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/727
`/scratch/stefan/7786831/working/3D/727' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(Cl)=CC=C2[O-])CC1)

`REAL300025051838.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051838.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051838/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051838 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(Cl)=CC=C2[O-])CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 68, 106, 191, 191, 191, 191, 191, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 3, 7, 7, 7, 1, 1, 68, 68, 191, 21, 6, 6, 3, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 498
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051838 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(Cl)=CC=C2[O-])CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 38, 13, 1, 1, 1, 1, 1, 1, 1, 90, 90, 165, 191, 199, 199, 199, 201, 201, 201, 199, 201, 201, 201, 191, 191, 38, 38, 1, 90, 165, 165, 199, 201, 201, 201, 191, 191, 191, 191] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 787
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051838 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(Cl)=CC=C2[O-])CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [35, 35, 35, 89, 129, 201, 201, 201, 201, 201, 17, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 89, 89, 201, 35, 17, 17, 4, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [33, 34, 35, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39])
total number of confs: 564
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051838 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051838
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051838/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051838/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051838
Building REAL300025051839
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051839'
/scratch/stefan/7786831/working/building/REAL300025051839 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051839

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051839/0 /scratch/stefan/7786831/working/building/REAL300025051839 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 728)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/728
`/scratch/stefan/7786831/working/3D/728' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(=O)CCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051839.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051839.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051839/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051839 none CCOC(=O)CCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 88, 201, 83, 77, 32, 32, 32, 32, 26, 26, 26, 20, 26, 12, 1, 1, 1, 1, 1, 1, 1, 32, 32, 201, 201, 201, 201, 201, 88, 88, 88, 88, 77, 77, 32, 26, 26, 26, 20, 20, 1, 32, 32, 32, 32] 201
rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47])
total number of confs: 714
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051839 none CCOC(=O)CCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [62, 62, 62, 11, 62, 10, 9, 2, 2, 2, 1, 1, 1, 3, 3, 3, 3, 7, 10, 32, 32, 32, 32, 32, 1, 1, 62, 62, 62, 62, 62, 11, 11, 11, 11, 9, 9, 2, 3, 3, 3, 7, 7, 32, 1, 1, 1, 1] 201
rigid atoms, others: [44, 10, 11, 12, 45, 46, 47, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 230
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051839 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051839
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051839/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051839
Building REAL300025051840
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051840'
/scratch/stefan/7786831/working/building/REAL300025051840 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051840

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051840/0 /scratch/stefan/7786831/working/building/REAL300025051840 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 729)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/729
`/scratch/stefan/7786831/working/3D/729' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(COC1=CC=CC=C1O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051840.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051840.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051840/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051840 none O=C(COC1=CC=CC=C1O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 12, 1, 1, 1, 1, 1, 1, 12, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
372  conformations in input
total number of sets (complete confs): 372
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 4, 17, 31, 31, 22, 31, 31, 31, 1, 1, 1, 4, 7, 7, 7, 28, 38, 96, 96, 96, 96, 96, 1, 1, 4, 4, 31, 31, 31, 31, 62, 2, 4, 4, 7, 28, 28, 96, 1, 1, 1, 1] 372
rigid atoms, others: [43, 41, 42, 11, 12, 13, 44, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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])
total number of confs: 356
number of broken/clashed sets: 101
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051840 none O=C(COC1=CC=CC=C1O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 12, 1, 1, 1, 1, 1, 1, 12, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
372  conformations in input
total number of sets (complete confs): 372
using faster count positions algorithm for large data
unique positions, atoms: [31, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 48, 52, 52, 52, 108, 131, 186, 186, 186, 186, 186, 31, 31, 21, 21, 1, 1, 1, 1, 2, 31, 48, 48, 52, 108, 108, 186, 31, 31, 31, 31] 372
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, 40, 41, 42, 43, 44])
total number of confs: 618
number of broken/clashed sets: 101
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051840 none O=C(COC1=CC=CC=C1O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 12, 1, 1, 1, 1, 1, 1, 12, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
372  conformations in input
total number of sets (complete confs): 372
using faster count positions algorithm for large data
unique positions, atoms: [96, 96, 96, 126, 175, 186, 186, 186, 186, 186, 186, 96, 90, 73, 73, 45, 73, 13, 1, 1, 1, 1, 1, 1, 1, 96, 96, 126, 126, 186, 186, 186, 186, 372, 96, 90, 90, 73, 45, 45, 1, 96, 96, 96, 96] 372
rigid atoms, others: [40, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 1003
number of broken/clashed sets: 101
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051840 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051840
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051840/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051840
Building REAL300025051841
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051841'
/scratch/stefan/7786831/working/building/REAL300025051841 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051841

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051841/0 /scratch/stefan/7786831/working/building/REAL300025051841 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 730)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/730
`/scratch/stefan/7786831/working/3D/730' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=CC=C1)

`REAL300025051841.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051841.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051841/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051841 none CCC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 169, 169, 169, 169, 132, 53, 53, 27, 53, 13, 1, 1, 1, 1, 1, 1, 1, 169, 169, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 169, 132, 132, 53, 27, 27, 1, 169, 169, 169, 169, 201, 201, 201, 201, 201] 201
rigid atoms, others: [39, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 813
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051841 none CCC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 5, 2, 2, 2, 1, 1, 1, 7, 24, 24, 24, 73, 85, 169, 169, 169, 169, 169, 1, 1, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 5, 2, 7, 7, 24, 73, 73, 169, 1, 1, 1, 1, 5, 5, 5, 5, 5] 201
rigid atoms, others: [5, 6, 7, 40, 41, 42, 43, 19, 20] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48])
total number of confs: 456
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051841 none CCC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 5, 5, 5, 5, 17, 43, 43, 43, 115, 127, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 3, 5, 17, 17, 43, 115, 115, 201, 5, 5, 5, 5, 1, 1, 1, 1, 1] 201
rigid atoms, others: [2, 44, 45, 46, 47, 48, 21, 22, 23, 24, 25, 26] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 621
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051841 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051841
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051841/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051841
Building REAL300025051842
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051842'
/scratch/stefan/7786831/working/building/REAL300025051842 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051842

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051842/0 /scratch/stefan/7786831/working/building/REAL300025051842 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 731)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/731
`/scratch/stefan/7786831/working/3D/731' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051842.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051842.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051842/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051842 none NC(=O)C=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 147, 65, 65, 32, 65, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 147, 147, 65, 32, 32, 1, 201, 201, 201, 201] 201
rigid atoms, others: [33, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 781
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051842 none NC(=O)C=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 6, 11, 6, 2, 2, 2, 1, 1, 1, 7, 21, 21, 21, 75, 102, 201, 201, 201, 201, 201, 1, 1, 11, 11, 6, 6, 2, 7, 7, 21, 75, 75, 201, 1, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 528
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051842 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051842
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051842/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051842
Building REAL300025051843
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051843'
/scratch/stefan/7786831/working/building/REAL300025051843 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051843

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051843/0 /scratch/stefan/7786831/working/building/REAL300025051843 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 732)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/732
`/scratch/stefan/7786831/working/3D/732' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=NC=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051843.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051843.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051843/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051843 none NC1=NC=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 6, 21, 21, 21, 57, 68, 138, 138, 138, 138, 138, 1, 1, 7, 7, 7, 7, 7, 2, 6, 6, 21, 57, 57, 138, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
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: REAL300025051843 none NC1=NC=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 21, 55, 55, 55, 112, 126, 201, 201, 201, 201, 201, 7, 7, 2, 2, 1, 1, 1, 7, 21, 21, 55, 112, 112, 201, 7, 7, 7, 7] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 583
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051843 none NC1=NC=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 138, 138, 138, 138, 94, 53, 53, 26, 53, 13, 1, 1, 1, 1, 1, 1, 1, 138, 138, 201, 201, 201, 201, 201, 138, 94, 94, 53, 26, 26, 1, 138, 138, 138, 138] 201
rigid atoms, others: [36, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 627
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051843 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051843
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051843/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051843
Building REAL300025051844
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051844'
/scratch/stefan/7786831/working/building/REAL300025051844 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051844

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051844/0 /scratch/stefan/7786831/working/building/REAL300025051844 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 733)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/733
`/scratch/stefan/7786831/working/3D/733' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1)

`REAL300025051844.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051844.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051844/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051844 none NC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 7, 29, 29, 29, 97, 117, 201, 201, 201, 201, 201, 1, 1, 3, 3, 3, 3, 2, 7, 7, 29, 97, 97, 201, 1, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 552
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051844 none NC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 10, 34, 34, 34, 102, 121, 201, 201, 201, 201, 201, 3, 3, 1, 2, 2, 1, 3, 10, 10, 34, 102, 102, 201, 3, 3, 3, 3] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 23, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 572
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051844 none NC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 136, 61, 61, 29, 61, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 136, 136, 61, 29, 29, 1, 201, 201, 201, 201] 201
rigid atoms, others: [33, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 755
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051844 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051844
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051844/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051844
Building REAL300025051845
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051845'
/scratch/stefan/7786831/working/building/REAL300025051845 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051845

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051845/0 /scratch/stefan/7786831/working/building/REAL300025051845 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 734)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/734
`/scratch/stefan/7786831/working/3D/734' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C[N+]([O-])=C2)CC1)

`REAL300025051845.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051845.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051845/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051845 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C[N+]([O-])=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 12, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 25, 76, 88, 147, 147, 147, 147, 147, 6, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 1, 1, 76, 76, 147, 25, 6, 6, 3, 9, 9, 9, 9, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 407
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051845 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C[N+]([O-])=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 12, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [75, 31, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 115, 147, 147, 147, 147, 201, 201, 201, 201, 201, 201, 147, 147, 31, 31, 1, 75, 115, 115, 147, 201, 201, 201, 201, 147, 147, 147, 147] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 626
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051845 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C[N+]([O-])=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 12, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 152, 167, 201, 201, 201, 201, 201, 17, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 9, 9, 152, 152, 201, 67, 17, 17, 5, 1, 1, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39])
total number of confs: 679
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051845 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051845
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051845/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051845
Building REAL300025051846
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051846'
/scratch/stefan/7786831/working/building/REAL300025051846 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051846

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051846/0 /scratch/stefan/7786831/working/building/REAL300025051846 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 735)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/735
`/scratch/stefan/7786831/working/3D/735' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNC1=CC=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051846.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051846.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051846/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051846 none CNC1=CC=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 6, 14, 14, 14, 46, 63, 144, 144, 144, 144, 144, 1, 1, 12, 12, 12, 12, 9, 9, 9, 9, 2, 6, 6, 14, 46, 46, 144, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 10, 11, 12, 44, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 347
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: REAL300025051846 none CNC1=CC=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 24, 39, 39, 39, 93, 121, 201, 201, 201, 201, 201, 9, 9, 4, 4, 4, 4, 1, 1, 1, 1, 9, 24, 24, 39, 93, 93, 201, 9, 9, 9, 9] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 33, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 564
number of broken/clashed sets: 46
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051846 none CNC1=CC=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 144, 144, 144, 144, 116, 66, 66, 26, 66, 13, 1, 1, 1, 1, 1, 1, 1, 144, 144, 201, 201, 201, 201, 201, 201, 201, 201, 144, 116, 116, 66, 26, 26, 1, 144, 144, 144, 144] 201
rigid atoms, others: [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, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 662
number of broken/clashed sets: 46
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051846 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051846
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051846/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051846
Building REAL300025051847
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051847'
/scratch/stefan/7786831/working/building/REAL300025051847 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051847

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051847/0 /scratch/stefan/7786831/working/building/REAL300025051847 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 736)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/736
`/scratch/stefan/7786831/working/3D/736' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1N)

`REAL300025051847.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051847.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051847/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051847 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1N NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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: [5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 18, 18, 18, 55, 63, 110, 110, 110, 110, 110, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 18, 55, 55, 110, 1, 1, 1, 1, 5, 5, 5] 201
rigid atoms, others: [38, 7, 8, 9, 39, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 42, 43, 44])
total number of confs: 305
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051847 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1N NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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: [1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 60, 60, 60, 141, 155, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 2, 2, 2, 1, 1, 5, 13, 13, 60, 141, 141, 201, 5, 5, 5, 5, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 43, 44, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 662
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051847 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1N NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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, 201, 110, 110, 110, 110, 91, 54, 54, 26, 54, 13, 1, 1, 1, 1, 1, 1, 1, 110, 110, 201, 201, 201, 201, 201, 201, 201, 201, 110, 91, 91, 54, 26, 26, 1, 110, 110, 110, 110, 201, 201, 201] 201
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 560
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051847 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051847
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051847/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051847
Building REAL300025051848
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051848'
/scratch/stefan/7786831/working/building/REAL300025051848 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051848

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051848/0 /scratch/stefan/7786831/working/building/REAL300025051848 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 737)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/737
`/scratch/stefan/7786831/working/3D/737' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)N1C=C(Cl)C=N1)

`REAL300025051848.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051848.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051848/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051848 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)N1C=C(Cl)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 1, 16, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 169, 169, 169, 169, 118, 50, 50, 26, 50, 13, 1, 1, 1, 1, 1, 1, 1, 169, 169, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 169, 118, 118, 50, 26, 26, 1, 169, 169, 169, 169, 201, 201] 201
rigid atoms, others: [36, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42])
total number of confs: 802
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051848 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)N1C=C(Cl)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 1, 16, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 2, 2, 2, 1, 1, 1, 7, 26, 26, 26, 70, 79, 169, 169, 169, 169, 169, 1, 1, 7, 11, 11, 11, 11, 11, 7, 7, 7, 7, 2, 7, 7, 26, 70, 70, 169, 1, 1, 1, 1, 11, 11] 201
rigid atoms, others: [4, 5, 6, 39, 40, 18, 19, 38, 37] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42])
total number of confs: 453
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051848 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)N1C=C(Cl)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 1, 16, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 11, 11, 11, 11, 23, 55, 55, 55, 113, 124, 201, 201, 201, 201, 201, 11, 11, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 11, 23, 23, 55, 113, 113, 201, 11, 11, 11, 11, 1, 1] 201
rigid atoms, others: [1, 41, 42, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 611
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051848 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051848
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051848/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051848
Building REAL300025051849
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051849'
/scratch/stefan/7786831/working/building/REAL300025051849 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051849

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051849/0 /scratch/stefan/7786831/working/building/REAL300025051849 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 738)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/738
`/scratch/stefan/7786831/working/3D/738' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051849.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051849.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051849/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051849 none COC(=O)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 188, 201, 96, 96, 96, 96, 86, 56, 56, 24, 56, 12, 1, 1, 1, 1, 1, 1, 1, 96, 96, 201, 201, 201, 188, 188, 96, 86, 86, 56, 24, 24, 1, 96, 96, 96, 96] 201
rigid atoms, others: [34, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 851
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051849 none COC(=O)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [34, 34, 11, 34, 2, 2, 2, 1, 1, 1, 4, 6, 6, 6, 18, 28, 96, 96, 96, 96, 96, 1, 1, 34, 34, 34, 11, 11, 2, 4, 4, 6, 18, 18, 96, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 269
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051849 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051849
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051849/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051849
Building REAL300025051850
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051850'
/scratch/stefan/7786831/working/building/REAL300025051850 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051850

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051850/0 /scratch/stefan/7786831/working/building/REAL300025051850 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 739)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/739
`/scratch/stefan/7786831/working/3D/739' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(=O)NC=N2)CC1)

`REAL300025051850.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051850.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051850/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051850 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(=O)NC=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 30, 106, 116, 198, 198, 198, 198, 198, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 1, 1, 106, 106, 198, 30, 6, 6, 3, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
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: REAL300025051850 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(=O)NC=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [74, 32, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 151, 198, 198, 198, 198, 201, 201, 201, 201, 201, 201, 198, 198, 32, 32, 1, 74, 151, 151, 198, 201, 201, 201, 198, 198, 198, 198] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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])
total number of confs: 746
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051850 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(=O)NC=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [49, 49, 49, 124, 131, 201, 201, 201, 201, 201, 13, 7, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 124, 124, 201, 49, 13, 13, 4, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38])
total number of confs: 596
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051850 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051850
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051850/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051850
Building REAL300025051851
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051851'
/scratch/stefan/7786831/working/building/REAL300025051851 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051851

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051851/0 /scratch/stefan/7786831/working/building/REAL300025051851 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 740)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/740
`/scratch/stefan/7786831/working/3D/740' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCSCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051851.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051851.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051851/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051851 none C#CCSCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 14, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 171, 159, 93, 93, 93, 93, 78, 53, 53, 25, 53, 13, 1, 1, 1, 1, 1, 1, 1, 93, 93, 201, 201, 201, 159, 159, 93, 78, 78, 53, 25, 25, 1, 93, 93, 93, 93] 201
rigid atoms, others: [34, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 878
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051851 none C#CCSCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 14, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [39, 39, 16, 8, 2, 2, 2, 1, 1, 1, 3, 5, 5, 5, 16, 24, 93, 93, 93, 93, 93, 1, 1, 39, 39, 39, 8, 8, 2, 3, 3, 5, 16, 16, 93, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 309
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051851 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051851
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051851/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051851
Building REAL300025051852
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051852'
/scratch/stefan/7786831/working/building/REAL300025051852 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051852

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051852/0 /scratch/stefan/7786831/working/building/REAL300025051852 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 741)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/741
`/scratch/stefan/7786831/working/3D/741' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3NCCN3N=C2)CC1)

`REAL300025051852.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051852.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051852/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051852 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3NCCN3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 8, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
117  conformations in input
total number of sets (complete confs): 117
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 62, 76, 117, 117, 117, 117, 117, 5, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 1, 1, 62, 62, 117, 22, 5, 5, 3, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1] 117
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 331
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051852 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3NCCN3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 8, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
117  conformations in input
total number of sets (complete confs): 117
using faster count positions algorithm for large data
unique positions, atoms: [63, 33, 13, 1, 1, 1, 1, 1, 1, 1, 63, 63, 103, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 33, 33, 1, 63, 103, 103, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117] 117
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 442
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051852 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3NCCN3N=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 8, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 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: [32, 32, 32, 74, 87, 117, 117, 117, 117, 117, 10, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 74, 74, 117, 32, 10, 10, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 117
rigid atoms, others: [33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42])
total number of confs: 352
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051852 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051852
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051852/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051852
Building REAL300025051853
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051853'
/scratch/stefan/7786831/working/building/REAL300025051853 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051853

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051853/0 /scratch/stefan/7786831/working/building/REAL300025051853 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 742)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/742
`/scratch/stefan/7786831/working/3D/742' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSC=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051853.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051853.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051853/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051853 none CSC=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 200, 200, 182, 182, 182, 182, 151, 93, 93, 32, 93, 13, 1, 1, 1, 1, 1, 1, 1, 182, 182, 201, 201, 201, 200, 200, 182, 151, 151, 93, 32, 32, 1, 182, 182, 182, 182] 201
rigid atoms, others: [33, 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, 34, 35, 36, 37])
total number of confs: 764
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051853 none CSC=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 9, 9, 2, 2, 2, 1, 1, 1, 4, 12, 12, 12, 48, 80, 182, 182, 182, 182, 182, 1, 1, 22, 22, 22, 9, 9, 2, 4, 4, 12, 48, 48, 182, 1, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 20, 21] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 411
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051853 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051853
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051853/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051853
Building REAL300025051854
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051854'
/scratch/stefan/7786831/working/building/REAL300025051854 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051854

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051854/0 /scratch/stefan/7786831/working/building/REAL300025051854 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 743)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/743
`/scratch/stefan/7786831/working/3D/743' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CNC=CC2=O)CC1)

`REAL300025051854.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051854.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051854/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051854 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CNC=CC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 30, 92, 101, 201, 201, 201, 201, 201, 7, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 1, 1, 92, 92, 201, 30, 7, 7, 3, 5, 5, 5, 5, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 519
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051854 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CNC=CC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 31, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 152, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 31, 31, 1, 61, 152, 152, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 753
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051854 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CNC=CC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 48, 127, 134, 201, 201, 201, 201, 201, 11, 5, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 127, 127, 201, 48, 11, 11, 4, 1, 1, 1, 1, 5, 5, 5, 5] 201
rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39])
total number of confs: 621
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051854 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051854
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051854/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051854
Building REAL300025051855
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051855'
/scratch/stefan/7786831/working/building/REAL300025051855 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051855

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051855/0 /scratch/stefan/7786831/working/building/REAL300025051855 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 744)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/744
`/scratch/stefan/7786831/working/3D/744' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CS1)

`REAL300025051855.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051855.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051855/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051855 none CC1=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 14, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 2, 2, 2, 1, 1, 1, 7, 24, 24, 24, 63, 69, 183, 183, 183, 183, 183, 1, 1, 7, 7, 7, 7, 7, 7, 2, 7, 7, 24, 63, 63, 183, 1, 1, 1, 1, 7, 7] 201
rigid atoms, others: [35, 36, 37, 6, 7, 8, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40])
total number of confs: 433
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051855 none CC1=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 14, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 7, 20, 55, 55, 55, 125, 130, 201, 201, 201, 201, 201, 7, 7, 1, 1, 2, 2, 2, 1, 7, 20, 20, 55, 125, 125, 201, 7, 7, 7, 7, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 39, 40, 22, 23, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 630
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051855 none CC1=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 14, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 183, 183, 183, 183, 133, 46, 46, 26, 46, 13, 1, 1, 1, 1, 1, 1, 1, 183, 183, 201, 201, 201, 201, 201, 201, 183, 133, 133, 46, 26, 26, 1, 183, 183, 183, 183, 201, 201] 201
rigid atoms, others: [34, 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, 35, 36, 37, 38, 39, 40])
total number of confs: 765
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051855 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051855
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051855/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051855
Building REAL300025051856
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051856'
/scratch/stefan/7786831/working/building/REAL300025051856 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051856

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051856/0 /scratch/stefan/7786831/working/building/REAL300025051856 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 745)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/745
`/scratch/stefan/7786831/working/3D/745' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C(=O)C(F)(F)F)CC1)

`REAL300025051856.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051856.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051856/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051856 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C(=O)C(F)(F)F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 11, 5, 15, 15, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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, 12, 12, 31, 45, 84, 84, 84, 84, 84, 6, 1, 1, 1, 3, 3, 3, 16, 16, 16, 16, 16, 1, 1, 31, 31, 84, 12, 6, 6, 3, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 11, 12, 13, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30])
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: REAL300025051856 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C(=O)C(F)(F)F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 11, 5, 15, 15, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [52, 37, 13, 1, 1, 1, 1, 1, 1, 1, 52, 52, 80, 84, 84, 84, 84, 201, 201, 201, 201, 201, 84, 84, 37, 37, 1, 52, 80, 80, 84, 84, 84, 84, 84] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 678
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051856 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051856
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051856/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051856
Building REAL300025051857
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051857'
/scratch/stefan/7786831/working/building/REAL300025051857 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051857

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051857/0 /scratch/stefan/7786831/working/building/REAL300025051857 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 746)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/746
`/scratch/stefan/7786831/working/3D/746' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(Cl)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NN1)

`REAL300025051857.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051857.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051857/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051857 none CC1=C(Cl)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 6, 2, 2, 2, 1, 1, 1, 4, 21, 21, 21, 78, 88, 164, 164, 164, 164, 164, 1, 1, 6, 6, 6, 6, 6, 2, 4, 4, 21, 78, 78, 164, 1, 1, 1, 1, 6] 201
rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39])
total number of confs: 428
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051857 none CC1=C(Cl)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 11, 44, 44, 44, 125, 137, 201, 201, 201, 201, 201, 6, 6, 1, 1, 2, 2, 2, 6, 11, 11, 44, 125, 125, 201, 6, 6, 6, 6, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 23, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 609
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051857 none CC1=C(Cl)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 164, 164, 164, 164, 130, 71, 71, 32, 71, 13, 1, 1, 1, 1, 1, 1, 1, 164, 164, 201, 201, 201, 201, 201, 164, 130, 130, 71, 32, 32, 1, 164, 164, 164, 164, 201] 201
rigid atoms, others: [34, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39])
total number of confs: 675
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051857 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051857/1 /scratch/stefan/7786831/working/building/REAL300025051857 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 747)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/747
`/scratch/stefan/7786831/working/3D/747' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1Cl)

`REAL300025051857.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051857.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051857/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051857 none CC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 16, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 6, 2, 2, 2, 1, 1, 1, 7, 28, 28, 28, 96, 121, 167, 167, 167, 167, 167, 1, 1, 6, 6, 6, 6, 6, 6, 2, 7, 7, 28, 96, 96, 167, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 7, 8, 9, 39, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 474
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051857 none CC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 16, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 19, 53, 53, 53, 138, 165, 201, 201, 201, 201, 201, 6, 6, 1, 1, 2, 2, 2, 1, 6, 19, 19, 53, 138, 138, 201, 6, 6, 6, 6] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 23, 24, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 638
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051857 none CC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 16, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 167, 167, 167, 167, 144, 81, 81, 29, 81, 13, 1, 1, 1, 1, 1, 1, 1, 167, 167, 201, 201, 201, 201, 201, 201, 167, 144, 144, 81, 29, 29, 1, 167, 167, 167, 167] 201
rigid atoms, others: [35, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39])
total number of confs: 668
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051857 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051857
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051857/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051857/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051857
Building REAL300025051858
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051858'
/scratch/stefan/7786831/working/building/REAL300025051858 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051858

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051858/0 /scratch/stefan/7786831/working/building/REAL300025051858 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 748)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/748
`/scratch/stefan/7786831/working/3D/748' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C#N)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051858.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051858.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051858/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051858 none CC1=CC=C(C#N)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 7, 21, 21, 21, 46, 55, 136, 136, 136, 136, 136, 1, 1, 9, 9, 9, 9, 9, 9, 2, 7, 7, 21, 46, 46, 136, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 331
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051858 none CC1=CC=C(C#N)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 32, 54, 54, 54, 105, 117, 201, 201, 201, 201, 201, 9, 9, 2, 2, 2, 1, 1, 1, 9, 32, 32, 54, 105, 105, 201, 9, 9, 9, 9] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 30, 31] set([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: 624
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051858 none CC1=CC=C(C#N)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 136, 136, 136, 136, 93, 48, 48, 27, 48, 13, 1, 1, 1, 1, 1, 1, 1, 136, 136, 201, 201, 201, 201, 201, 201, 136, 93, 93, 48, 27, 27, 1, 136, 136, 136, 136] 201
rigid atoms, others: [39, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 625
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051858 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051858
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051858/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051858
Building REAL300025051859
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051859'
/scratch/stefan/7786831/working/building/REAL300025051859 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051859

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051859/0 /scratch/stefan/7786831/working/building/REAL300025051859 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 749)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/749
`/scratch/stefan/7786831/working/3D/749' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=NN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1)

`REAL300025051859.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051859.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051859/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051859 none NC1=NN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 12, 8, 2, 2, 2, 1, 1, 1, 6, 17, 17, 17, 55, 73, 158, 158, 158, 158, 158, 1, 1, 12, 12, 12, 12, 8, 8, 2, 6, 6, 17, 55, 55, 158, 1, 1, 1, 1, 12, 12] 201
rigid atoms, others: [36, 37, 38, 7, 8, 9, 39, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41])
total number of confs: 394
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051859 none NC1=NN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 28, 53, 53, 53, 108, 125, 201, 201, 201, 201, 201, 12, 12, 1, 1, 2, 2, 5, 5, 12, 28, 28, 53, 108, 108, 201, 12, 12, 12, 12, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 40, 41, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 623
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051859 none NC1=NN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 158, 158, 158, 158, 111, 58, 58, 29, 58, 13, 1, 1, 1, 1, 1, 1, 1, 158, 158, 201, 201, 201, 201, 201, 201, 158, 111, 111, 58, 29, 29, 1, 158, 158, 158, 158, 201, 201] 201
rigid atoms, others: [35, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41])
total number of confs: 825
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051859 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051859
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051859/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051859
Building REAL300025051860
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051860'
/scratch/stefan/7786831/working/building/REAL300025051860 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051860

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051860/0 /scratch/stefan/7786831/working/building/REAL300025051860 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 750)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/750
`/scratch/stefan/7786831/working/3D/750' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CN=C1N)

`REAL300025051860.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051860.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051860/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051860 none NC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CN=C1N NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 1, 8, 6, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [4, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 2, 2, 2, 1, 1, 1, 3, 20, 20, 20, 72, 89, 147, 147, 147, 147, 147, 1, 1, 5, 5, 5, 5, 5, 5, 5, 2, 3, 3, 20, 72, 72, 147, 1, 1, 1, 1, 5, 5, 5] 188
rigid atoms, others: [36, 37, 6, 7, 8, 39, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 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, 40, 41, 42])
total number of confs: 394
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051860 none NC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CN=C1N NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 1, 8, 6, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [4, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 49, 49, 49, 128, 148, 188, 188, 188, 188, 188, 5, 5, 1, 1, 1, 1, 2, 2, 1, 5, 13, 13, 49, 128, 128, 188, 5, 5, 5, 5, 1, 1, 1] 188
rigid atoms, others: [0, 1, 2, 3, 4, 40, 41, 42, 22, 23, 24, 25, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 598
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051860 none NC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CN=C1N NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 1, 8, 6, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [4, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [188, 188, 188, 147, 147, 147, 147, 124, 74, 74, 30, 74, 13, 1, 1, 1, 1, 1, 1, 1, 147, 147, 188, 188, 188, 188, 188, 188, 188, 147, 124, 124, 74, 30, 30, 1, 147, 147, 147, 147, 188, 188, 188] 188
rigid atoms, others: [35, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 630
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051860 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051860
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051860/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051860
Building REAL300025051861
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051861'
/scratch/stefan/7786831/working/building/REAL300025051861 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051861

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051861/0 /scratch/stefan/7786831/working/building/REAL300025051861 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 751)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/751
`/scratch/stefan/7786831/working/3D/751' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=CC(O)=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051861.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051861.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051861/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051861 none N#CC1=CC(O)=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 5, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 6, 23, 23, 23, 73, 84, 136, 136, 136, 136, 136, 1, 1, 5, 5, 10, 5, 2, 6, 6, 23, 73, 73, 136, 1, 1, 1, 1, 5] 402
rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41])
total number of confs: 390
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: REAL300025051861 none N#CC1=CC(O)=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 16, 61, 61, 61, 143, 156, 201, 201, 201, 201, 201, 5, 5, 1, 1, 2, 1, 5, 16, 16, 61, 143, 143, 201, 5, 5, 5, 5, 1] 402
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 26, 27, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 653
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051861 none N#CC1=CC(O)=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 136, 136, 136, 136, 111, 66, 66, 27, 66, 13, 1, 1, 1, 1, 1, 1, 1, 136, 136, 201, 201, 402, 201, 136, 111, 111, 66, 27, 27, 1, 136, 136, 136, 136, 201] 402
rigid atoms, others: [36, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41])
total number of confs: 1008
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051861 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051861/1 /scratch/stefan/7786831/working/building/REAL300025051861 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 752)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/752
`/scratch/stefan/7786831/working/3D/752' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=CC([O-])=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051861.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051861.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051861/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051861 none N#CC1=CC([O-])=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 7, 27, 27, 27, 67, 99, 145, 145, 145, 145, 145, 1, 1, 3, 3, 3, 2, 7, 7, 27, 67, 67, 145, 1, 1, 1, 1, 3] 201
rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40])
total number of confs: 393
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051861 none N#CC1=CC([O-])=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 12, 40, 40, 40, 99, 145, 201, 201, 201, 201, 201, 3, 3, 1, 1, 1, 3, 12, 12, 40, 99, 99, 201, 3, 3, 3, 3, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 40, 26, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 558
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051861 none N#CC1=CC([O-])=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 145, 145, 145, 145, 129, 79, 79, 38, 79, 13, 1, 1, 1, 1, 1, 1, 1, 145, 145, 201, 201, 201, 145, 129, 129, 79, 38, 38, 1, 145, 145, 145, 145, 201] 201
rigid atoms, others: [35, 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, 36, 37, 38, 39, 40])
total number of confs: 662
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051861 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051861
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051861/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051861/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051861
Building REAL300025051862
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051862'
/scratch/stefan/7786831/working/building/REAL300025051862 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051862

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051862/0 /scratch/stefan/7786831/working/building/REAL300025051862 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 753)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/753
`/scratch/stefan/7786831/working/3D/753' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCCC2O)CC1)

`REAL300025051862.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051862.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051862/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051862 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCCC2O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 85, 103, 181, 181, 181, 181, 181, 5, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 1, 1, 85, 85, 181, 24, 5, 5, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 33, 1, 1, 1, 1] 603
rigid atoms, others: [11, 44, 43, 12, 13, 46, 45, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 527
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051862 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCCC2O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [83, 35, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 150, 181, 181, 181, 181, 201, 201, 201, 201, 201, 201, 181, 181, 35, 35, 1, 83, 150, 150, 181, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 603, 181, 181, 181, 181] 603
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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, 45, 46])
total number of confs: 1346
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051862 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCCC2O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [63, 63, 63, 145, 159, 201, 201, 201, 201, 201, 17, 11, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 145, 145, 201, 63, 17, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 11, 11, 11, 11] 603
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 42, 43, 44, 45, 46])
total number of confs: 667
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051862 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051862
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051862/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051862
Building REAL300025051863
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051863'
/scratch/stefan/7786831/working/building/REAL300025051863 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051863

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051863/0 /scratch/stefan/7786831/working/building/REAL300025051863 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 754)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/754
`/scratch/stefan/7786831/working/3D/754' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CN=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051863.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051863.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051863/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051863 none CN1C=CN=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 10, 10, 8, 2, 2, 2, 1, 1, 1, 7, 21, 21, 21, 52, 71, 160, 160, 160, 160, 160, 1, 1, 10, 10, 10, 10, 10, 8, 8, 2, 7, 7, 21, 52, 52, 160, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 391
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051863 none CN1C=CN=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 10, 10, 10, 10, 26, 47, 47, 47, 98, 120, 201, 201, 201, 201, 201, 10, 10, 2, 2, 2, 1, 1, 3, 3, 10, 26, 26, 47, 98, 98, 201, 10, 10, 10, 10] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 603
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051863 none CN1C=CN=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 160, 160, 160, 160, 115, 68, 68, 29, 68, 13, 1, 1, 1, 1, 1, 1, 1, 160, 160, 201, 201, 201, 201, 201, 201, 201, 160, 115, 115, 68, 29, 29, 1, 160, 160, 160, 160] 201
rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 813
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051863 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051863
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051863/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051863
Building REAL300025051864
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051864'
/scratch/stefan/7786831/working/building/REAL300025051864 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051864

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051864/0 /scratch/stefan/7786831/working/building/REAL300025051864 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 755)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/755
`/scratch/stefan/7786831/working/3D/755' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)[N+](=O)[O-])

`REAL300025051864.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051864.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051864/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051864 none CC(C)(CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 196, 201, 196, 117, 117, 117, 117, 100, 63, 63, 29, 63, 13, 1, 1, 1, 1, 1, 1, 1, 117, 117, 201, 201, 201, 201, 201, 201, 201, 201, 201, 196, 196, 196, 196, 117, 100, 100, 63, 29, 29, 1, 117, 117, 117, 117] 201
rigid atoms, others: [42, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46])
total number of confs: 902
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051864 none CC(C)(CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
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, 9, 2, 2, 2, 1, 1, 1, 4, 6, 6, 6, 19, 30, 117, 117, 117, 117, 117, 1, 1, 13, 24, 24, 13, 13, 13, 13, 13, 13, 9, 9, 9, 9, 2, 4, 4, 6, 19, 19, 117, 1, 1, 1, 1] 201
rigid atoms, others: [7, 8, 9, 43, 44, 45, 46, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 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, 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/7786831/working/building/REAL300025051864 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051864
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051864/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051864
Building REAL300025051865
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051865'
/scratch/stefan/7786831/working/building/REAL300025051865 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051865

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051865/0 /scratch/stefan/7786831/working/building/REAL300025051865 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 756)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/756
`/scratch/stefan/7786831/working/3D/756' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(=O)CSC1=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051865.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051865.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051865/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051865 none CN1C(=O)CSC1=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 14, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 7, 20, 20, 20, 56, 70, 170, 171, 171, 171, 171, 1, 1, 9, 9, 9, 9, 9, 9, 2, 7, 7, 20, 56, 56, 171, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 10, 11, 12, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 408
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051865 none CN1C(=O)CSC1=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 14, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 25, 53, 53, 53, 113, 131, 201, 201, 201, 201, 201, 9, 9, 2, 2, 2, 1, 1, 1, 9, 25, 25, 53, 113, 113, 201, 9, 9, 9, 9] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([9, 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, 41, 42])
total number of confs: 620
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051865 none CN1C(=O)CSC1=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 14, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 171, 171, 171, 171, 124, 56, 56, 29, 56, 13, 1, 1, 1, 1, 1, 1, 1, 171, 171, 201, 201, 201, 201, 201, 201, 171, 124, 124, 56, 29, 29, 1, 171, 171, 171, 171] 201
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42])
total number of confs: 763
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051865 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051865
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051865/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051865
Building REAL300025051866
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051866'
/scratch/stefan/7786831/working/building/REAL300025051866 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051866

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051866/0 /scratch/stefan/7786831/working/building/REAL300025051866 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 757)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/757
`/scratch/stefan/7786831/working/3D/757' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC[N@@H+]1C)

`REAL300025051866.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051866.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051866/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051866 none CC1C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC[N@@H+]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 2, 2, 2, 1, 1, 1, 4, 6, 6, 6, 9, 10, 15, 15, 15, 15, 15, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 6, 9, 9, 15, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5] 15
rigid atoms, others: [5, 38, 7, 40, 41, 39, 19, 20, 6] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48])
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: REAL300025051866 none CC1C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC[N@@H+]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 5, 5, 5, 5, 6, 8, 8, 8, 10, 11, 15, 15, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 5, 6, 6, 8, 10, 10, 15, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2] 15
rigid atoms, others: [0, 1, 2, 3, 42, 43, 44, 45, 21, 22, 23, 24, 25, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48])
total number of confs: 56
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051866 none CC1C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC[N@@H+]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 14, 14, 11, 14, 7, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 11, 11, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 15
rigid atoms, others: [37, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 48
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051866 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051866/1 /scratch/stefan/7786831/working/building/REAL300025051866 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 758)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/758
`/scratch/stefan/7786831/working/3D/758' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC[N@H+]1C)

`REAL300025051866.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051866.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051866/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051866 none CC1C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC[N@H+]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 2, 2, 2, 1, 1, 1, 4, 6, 6, 6, 9, 10, 15, 15, 15, 15, 15, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 6, 9, 9, 15, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5] 15
rigid atoms, others: [5, 38, 7, 40, 41, 39, 19, 20, 6] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48])
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: REAL300025051866 none CC1C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC[N@H+]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 5, 5, 5, 5, 6, 8, 8, 8, 10, 11, 15, 15, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 5, 6, 6, 8, 10, 10, 15, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2] 15
rigid atoms, others: [0, 1, 2, 3, 42, 43, 44, 45, 21, 22, 23, 24, 25, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48])
total number of confs: 56
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051866 none CC1C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC[N@H+]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 14, 14, 11, 14, 7, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 11, 11, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 15
rigid atoms, others: [37, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 48
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051866 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051866
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051866/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051866/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051866
Building REAL300025051867
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051867'
/scratch/stefan/7786831/working/building/REAL300025051867 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051867

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051867/0 /scratch/stefan/7786831/working/building/REAL300025051867 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 759)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/759
`/scratch/stefan/7786831/working/3D/759' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=CC(=O)N2)CC1)

`REAL300025051867.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051867.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051867/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051867 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=CC(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 19, 56, 71, 121, 121, 121, 121, 121, 5, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 1, 1, 56, 56, 121, 19, 5, 5, 3, 15, 15, 15, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 335
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051867 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=CC(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 31, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 102, 121, 121, 121, 121, 201, 201, 201, 201, 201, 201, 121, 121, 31, 31, 1, 61, 102, 102, 121, 201, 201, 201, 121, 121, 121, 121] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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])
total number of confs: 570
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051867 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=CC(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [71, 71, 71, 145, 163, 201, 201, 201, 201, 201, 25, 15, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 15, 15, 145, 145, 201, 71, 25, 25, 9, 1, 1, 1, 15, 15, 15, 15] 201
rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38])
total number of confs: 692
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051867 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051867
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051867/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051867
Building REAL300025051868
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051868'
/scratch/stefan/7786831/working/building/REAL300025051868 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051868

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051868/0 /scratch/stefan/7786831/working/building/REAL300025051868 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 760)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/760
`/scratch/stefan/7786831/working/3D/760' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@@H+]1CCCCC1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051868.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051868.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051868/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051868 none C[N@@H+]1CCCCC1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
5  conformations in input
total number of sets (complete confs): 5
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 3, 4, 5, 5, 5, 5, 5, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 5, 1, 1, 1, 1] 5
rigid atoms, others: [12, 13, 14, 51, 52, 53, 54, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 25
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: REAL300025051868 none C[N@@H+]1CCCCC1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 5, 5, 5, 5, 5, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 3, 3, 3, 3] 5
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 34, 35, 32, 36, 33, 38, 37, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 20
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051868 none C[N@@H+]1CCCCC1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
5  conformations in input
total number of sets (complete confs): 5
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 5, 5, 5, 5] 5
rigid atoms, others: [50, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54])
total number of confs: 6
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051868 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051868/1 /scratch/stefan/7786831/working/building/REAL300025051868 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 761)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/761
`/scratch/stefan/7786831/working/3D/761' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@H+]1CCCCC1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051868.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051868.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051868/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051868 none C[N@H+]1CCCCC1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 7, 6, 2, 2, 2, 1, 1, 1, 6, 12, 12, 12, 23, 35, 52, 52, 52, 52, 52, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 6, 6, 2, 6, 6, 12, 23, 23, 52, 1, 1, 1, 1] 53
rigid atoms, others: [12, 13, 14, 51, 52, 53, 54, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 165
number of broken/clashed sets: 50
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051868 none C[N@H+]1CCCCC1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 4, 8, 8, 8, 8, 10, 14, 14, 14, 24, 36, 53, 53, 53, 53, 53, 8, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 7, 10, 10, 14, 24, 24, 53, 8, 8, 8, 8] 53
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 34, 35, 32, 36, 33, 38, 37, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 154
number of broken/clashed sets: 50
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051868 none C[N@H+]1CCCCC1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 52, 52, 52, 52, 52, 52, 47, 47, 27, 47, 12, 1, 1, 1, 1, 1, 1, 1, 52, 52, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 52, 52, 52, 52, 52, 47, 27, 27, 1, 52, 52, 52, 52] 53
rigid atoms, others: [50, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54])
total number of confs: 186
number of broken/clashed sets: 50
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051868 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051868
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051868/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051868/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051868
Building REAL300025051869
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051869'
/scratch/stefan/7786831/working/building/REAL300025051869 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051869

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051869/0 /scratch/stefan/7786831/working/building/REAL300025051869 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 762)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/762
`/scratch/stefan/7786831/working/3D/762' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CNC(=O)S2)CC1)

`REAL300025051869.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051869.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051869/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051869 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CNC(=O)S2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 31, 31, 99, 110, 201, 201, 201, 201, 201, 7, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 1, 99, 99, 201, 31, 7, 7, 3, 8, 8, 1, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 541
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051869 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CNC(=O)S2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [64, 34, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 147, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 34, 34, 1, 64, 147, 147, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 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])
total number of confs: 733
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051869 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CNC(=O)S2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [54, 54, 54, 133, 140, 201, 201, 201, 201, 201, 14, 8, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 133, 133, 201, 54, 14, 14, 6, 1, 1, 8, 8, 8, 8] 201
rigid atoms, others: [32, 14, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36])
total number of confs: 626
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051869 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051869
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051869/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051869
Building REAL300025051870
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051870'
/scratch/stefan/7786831/working/building/REAL300025051870 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051870

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051870/0 /scratch/stefan/7786831/working/building/REAL300025051870 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 763)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/763
`/scratch/stefan/7786831/working/3D/763' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1N)

`REAL300025051870.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051870.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051870/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051870 none CCC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1N NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [16, 9, 9, 5, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 9, 28, 40, 95, 95, 95, 95, 95, 1, 1, 9, 9, 16, 16, 16, 16, 16, 9, 9, 9, 2, 5, 5, 9, 28, 28, 95, 1, 1, 1, 1, 9, 9] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47])
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: REAL300025051870 none CCC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1N NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 19, 27, 27, 27, 49, 68, 122, 122, 122, 122, 122, 9, 9, 1, 1, 3, 3, 3, 3, 3, 1, 1, 1, 9, 19, 19, 27, 49, 49, 122, 9, 9, 9, 9, 2, 2] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 25, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 340
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051870 none CCC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1N NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 122, 122, 121, 122, 122, 95, 95, 95, 95, 84, 54, 54, 26, 54, 13, 1, 1, 1, 1, 1, 1, 1, 95, 95, 122, 122, 201, 201, 201, 201, 201, 122, 122, 122, 95, 84, 84, 54, 26, 26, 1, 95, 95, 95, 95, 122, 122] 201
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47])
total number of confs: 886
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051870 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051870
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051870/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051870
Building REAL300025051871
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051871'
/scratch/stefan/7786831/working/building/REAL300025051871 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051871

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051871/0 /scratch/stefan/7786831/working/building/REAL300025051871 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 764)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/764
`/scratch/stefan/7786831/working/3D/764' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051871.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051871.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051871/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051871 none NC(=O)CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 200, 171, 171, 171, 171, 141, 81, 81, 33, 81, 13, 1, 1, 1, 1, 1, 1, 1, 171, 171, 201, 201, 201, 201, 200, 200, 171, 141, 141, 81, 33, 33, 1, 171, 171, 171, 171] 201
rigid atoms, others: [35, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39])
total number of confs: 808
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051871 none NC(=O)CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 9, 16, 8, 2, 2, 2, 1, 1, 1, 6, 18, 18, 18, 56, 87, 171, 171, 171, 171, 171, 1, 1, 16, 16, 9, 9, 8, 8, 2, 6, 6, 18, 56, 56, 171, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 7, 8, 9, 39, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 448
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051871 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051871
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051871/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051871
Building REAL300025051872
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051872'
/scratch/stefan/7786831/working/building/REAL300025051872 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051872

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051872/0 /scratch/stefan/7786831/working/building/REAL300025051872 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 765)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/765
`/scratch/stefan/7786831/working/3D/765' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(COC(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051872.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051872.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051872/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051872 none O=C(COC(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 5, 15, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [68, 68, 68, 165, 201, 201, 201, 68, 60, 47, 47, 24, 47, 13, 1, 1, 1, 1, 1, 1, 1, 68, 68, 165, 165, 201, 68, 60, 60, 47, 24, 24, 1, 68, 68, 68, 68] 201
rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 746
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051872 none O=C(COC(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 5, 15, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 12, 34, 57, 57, 1, 1, 1, 4, 14, 14, 14, 30, 33, 68, 68, 68, 68, 68, 1, 1, 12, 12, 57, 2, 4, 4, 14, 30, 30, 68, 1, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 360
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051872 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051872
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051872/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051872
Building REAL300025051873
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051873'
/scratch/stefan/7786831/working/building/REAL300025051873 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051873

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051873/0 /scratch/stefan/7786831/working/building/REAL300025051873 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 766)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/766
`/scratch/stefan/7786831/working/3D/766' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C#N)C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051873.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051873.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051873/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051873 none CC1=C(C#N)C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 6, 19, 19, 19, 50, 59, 152, 152, 152, 152, 152, 1, 1, 9, 9, 9, 9, 9, 9, 2, 6, 6, 19, 50, 50, 152, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051873 none CC1=C(C#N)C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 29, 59, 59, 59, 114, 128, 201, 201, 201, 201, 201, 9, 9, 2, 2, 2, 1, 1, 1, 9, 29, 29, 59, 114, 114, 201, 9, 9, 9, 9] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 30, 31] set([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: 608
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051873 none CC1=C(C#N)C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 152, 152, 152, 152, 109, 56, 56, 27, 56, 13, 1, 1, 1, 1, 1, 1, 1, 152, 152, 201, 201, 201, 201, 201, 201, 152, 109, 109, 56, 27, 27, 1, 152, 152, 152, 152] 201
rigid atoms, others: [39, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 651
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051873 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051873
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051873/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051873
Building REAL300025051874
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051874'
/scratch/stefan/7786831/working/building/REAL300025051874 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051874

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051874/0 /scratch/stefan/7786831/working/building/REAL300025051874 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 767)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/767
`/scratch/stefan/7786831/working/3D/767' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CSC(NCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1)

`REAL300025051874.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051874.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051874/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051874 none CC1=CSC(NCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 14, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 11, 9, 5, 2, 2, 2, 1, 1, 1, 7, 18, 18, 18, 54, 89, 173, 173, 173, 173, 173, 1, 1, 11, 11, 11, 11, 11, 9, 5, 5, 2, 7, 7, 18, 54, 54, 173, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 428
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: REAL300025051874 none CC1=CSC(NCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 14, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 6, 11, 11, 11, 11, 24, 42, 42, 42, 87, 121, 201, 201, 201, 201, 201, 11, 11, 1, 2, 2, 2, 1, 3, 6, 6, 11, 24, 24, 42, 87, 87, 201, 11, 11, 11, 11] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 29] set([6, 7, 8, 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])
total number of confs: 546
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051874 none CC1=CSC(NCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 14, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 199, 173, 173, 173, 173, 148, 104, 104, 54, 104, 13, 1, 1, 1, 1, 1, 1, 1, 173, 173, 201, 201, 201, 201, 201, 201, 199, 199, 173, 148, 148, 104, 54, 54, 1, 173, 173, 173, 173] 201
rigid atoms, others: [39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 836
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051874 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051874
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051874/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051874
Building REAL300025051875
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051875'
/scratch/stefan/7786831/working/building/REAL300025051875 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051875

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051875/0 /scratch/stefan/7786831/working/building/REAL300025051875 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 768)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/768
`/scratch/stefan/7786831/working/3D/768' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CSCC2=NC=CN2)CC1)

`REAL300025051875.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051875.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051875/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051875 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CSCC2=NC=CN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 14, 5, 1, 8, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 30, 30, 46, 46, 46, 46, 46, 5, 1, 1, 1, 3, 3, 3, 18, 41, 70, 83, 83, 83, 83, 1, 1, 30, 30, 46, 16, 5, 5, 3, 18, 18, 70, 70, 83, 83, 83, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 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: REAL300025051875 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CSCC2=NC=CN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 14, 5, 1, 8, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 15, 13, 1, 1, 1, 1, 1, 1, 1, 22, 22, 41, 46, 46, 46, 46, 119, 165, 201, 201, 201, 201, 201, 46, 46, 15, 15, 1, 22, 41, 41, 46, 119, 119, 201, 201, 201, 201, 201, 46, 46, 46, 46] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 727
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051875 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CSCC2=NC=CN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 14, 5, 1, 8, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [147, 147, 147, 194, 194, 201, 201, 201, 201, 201, 85, 68, 59, 59, 27, 59, 15, 5, 1, 1, 1, 1, 1, 1, 68, 68, 194, 194, 201, 147, 85, 85, 59, 27, 27, 5, 5, 1, 1, 1, 68, 68, 68, 68] 201
rigid atoms, others: [37, 38, 39, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43])
total number of confs: 818
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051875 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051875
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051875/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051875
Building REAL300025051876
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051876'
/scratch/stefan/7786831/working/building/REAL300025051876 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051876

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051876/0 /scratch/stefan/7786831/working/building/REAL300025051876 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 769)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/769
`/scratch/stefan/7786831/working/3D/769' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CCCS2)CC1)

`REAL300025051876.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051876.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051876/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051876 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CCCS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 30, 96, 114, 199, 199, 199, 199, 199, 7, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 1, 1, 96, 96, 199, 30, 7, 7, 3, 9, 9, 9, 9, 9, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 532
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051876 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CCCS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [72, 35, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 159, 199, 199, 199, 199, 201, 201, 201, 201, 199, 199, 35, 35, 1, 72, 159, 159, 199, 201, 201, 201, 201, 201, 199, 199, 199, 199] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 25] set([0, 1, 2, 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: 751
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051876 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CCCS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [51, 51, 51, 127, 141, 201, 201, 201, 201, 201, 16, 9, 7, 7, 1, 7, 1, 1, 1, 1, 1, 9, 9, 127, 127, 201, 51, 16, 16, 7, 1, 1, 1, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38])
total number of confs: 614
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051876 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051876
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051876/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051876
Building REAL300025051877
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051877'
/scratch/stefan/7786831/working/building/REAL300025051877 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051877

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051877/0 /scratch/stefan/7786831/working/building/REAL300025051877 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 770)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/770
`/scratch/stefan/7786831/working/3D/770' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025051877.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051877.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051877/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051877 none CC1=NOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 7, 28, 28, 28, 76, 88, 184, 184, 184, 184, 184, 1, 1, 7, 7, 7, 7, 7, 2, 7, 7, 28, 76, 76, 184, 1, 1, 1, 1, 7, 7] 201
rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40])
total number of confs: 473
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051877 none CC1=NOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 25, 64, 64, 64, 128, 142, 201, 201, 201, 201, 201, 7, 7, 1, 2, 2, 2, 1, 7, 25, 25, 64, 128, 128, 201, 7, 7, 7, 7, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 40, 23, 27] set([6, 7, 8, 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, 37, 38])
total number of confs: 647
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051877 none CC1=NOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 184, 184, 184, 184, 136, 54, 54, 28, 54, 13, 1, 1, 1, 1, 1, 1, 1, 184, 184, 201, 201, 201, 201, 201, 184, 136, 136, 54, 28, 28, 1, 184, 184, 184, 184, 201, 201] 201
rigid atoms, others: [34, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40])
total number of confs: 750
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051877 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051877
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051877/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051877
Building REAL300025051878
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051878'
/scratch/stefan/7786831/working/building/REAL300025051878 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051878

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051878/0 /scratch/stefan/7786831/working/building/REAL300025051878 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 771)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/771
`/scratch/stefan/7786831/working/3D/771' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C(=O)NC2CC2)CC1)

`REAL300025051878.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051878.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051878/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051878 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C(=O)NC2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 20, 49, 55, 129, 129, 129, 129, 129, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 22, 22, 1, 1, 49, 49, 129, 20, 6, 6, 3, 7, 22, 22, 22, 22, 22, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 366
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051878 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C(=O)NC2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [50, 28, 12, 1, 1, 1, 1, 1, 1, 1, 50, 50, 100, 129, 129, 129, 129, 141, 141, 141, 201, 201, 129, 129, 28, 28, 1, 50, 100, 100, 129, 141, 201, 201, 201, 201, 201, 129, 129, 129, 129] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 767
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051878 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C(=O)NC2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [82, 82, 82, 139, 144, 201, 201, 201, 201, 201, 37, 22, 17, 17, 6, 17, 6, 6, 1, 1, 1, 1, 22, 22, 139, 139, 201, 82, 37, 37, 17, 6, 1, 1, 1, 1, 1, 22, 22, 22, 22] 201
rigid atoms, others: [32, 33, 34, 35, 36, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40])
total number of confs: 675
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051878 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051878
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051878/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051878
Building REAL300025051879
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051879'
/scratch/stefan/7786831/working/building/REAL300025051879 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051879

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051879/0 /scratch/stefan/7786831/working/building/REAL300025051879 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 772)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/772
`/scratch/stefan/7786831/working/3D/772' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C=C(Cl)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1)

`REAL300025051879.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051879.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051879/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051879 none CCN1C=C(Cl)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 4, 15, 15, 15, 43, 49, 99, 99, 99, 99, 99, 1, 1, 4, 7, 7, 7, 7, 7, 4, 2, 4, 4, 15, 43, 43, 99, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 278
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051879 none CCN1C=C(Cl)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 8, 25, 25, 25, 58, 64, 112, 112, 112, 112, 112, 4, 4, 1, 3, 3, 3, 3, 3, 1, 4, 8, 8, 25, 58, 58, 112, 4, 4, 4, 4] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 25, 31] set([0, 8, 9, 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])
total number of confs: 322
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051879 none CCN1C=C(Cl)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 112, 112, 112, 112, 112, 99, 99, 99, 99, 87, 58, 58, 30, 58, 13, 1, 1, 1, 1, 1, 1, 1, 99, 99, 112, 201, 201, 201, 201, 201, 112, 99, 87, 87, 58, 30, 30, 1, 99, 99, 99, 99] 201
rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 936
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051879 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051879
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051879/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051879
Building REAL300025051880
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051880'
/scratch/stefan/7786831/working/building/REAL300025051880 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051880

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051880/0 /scratch/stefan/7786831/working/building/REAL300025051880 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 773)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/773
`/scratch/stefan/7786831/working/3D/773' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=C(Cl)C=N2)CC1)

`REAL300025051880.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051880.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051880/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051880 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=C(Cl)C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 16, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 30, 113, 127, 201, 201, 201, 201, 201, 6, 1, 1, 1, 3, 3, 3, 7, 7, 3, 3, 7, 7, 1, 1, 113, 113, 201, 30, 6, 6, 3, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 574
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051880 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=C(Cl)C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 16, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [74, 32, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 157, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 32, 32, 1, 74, 157, 157, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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])
total number of confs: 765
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051880 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=C(Cl)C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 16, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 38, 38, 115, 134, 201, 201, 201, 201, 201, 15, 10, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 10, 10, 115, 115, 201, 38, 15, 15, 7, 1, 1, 10, 10, 10, 10] 201
rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37])
total number of confs: 571
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051880 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051880
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051880/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051880
Building REAL300025051881
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051881'
/scratch/stefan/7786831/working/building/REAL300025051881 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051881

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051881/0 /scratch/stefan/7786831/working/building/REAL300025051881 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 774)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/774
`/scratch/stefan/7786831/working/3D/774' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=NOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025051881.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051881.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051881/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051881 none CCC1=NOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 6, 6, 6, 22, 38, 139, 139, 139, 139, 139, 1, 1, 5, 28, 28, 28, 28, 28, 5, 2, 4, 4, 6, 22, 22, 139, 1, 1, 1, 1, 5, 5] 201
rigid atoms, others: [38, 39, 8, 9, 10, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 42, 43])
total number of confs: 340
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051881 none CCC1=NOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 16, 16, 16, 50, 75, 185, 185, 185, 185, 185, 5, 5, 1, 11, 11, 11, 10, 10, 1, 5, 10, 10, 16, 50, 50, 185, 5, 5, 5, 5, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 42, 43, 24, 30] set([0, 7, 8, 9, 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, 40, 41])
total number of confs: 450
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051881 none CCC1=NOC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 185, 185, 185, 185, 139, 139, 139, 139, 108, 65, 65, 29, 65, 13, 1, 1, 1, 1, 1, 1, 1, 139, 139, 185, 201, 201, 201, 201, 201, 185, 139, 108, 108, 65, 29, 29, 1, 139, 139, 139, 139, 185, 185] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43])
total number of confs: 822
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051881 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051881
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051881/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051881
Building REAL300025051882
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051882'
/scratch/stefan/7786831/working/building/REAL300025051882 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051882

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051882/0 /scratch/stefan/7786831/working/building/REAL300025051882 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 775)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/775
`/scratch/stefan/7786831/working/3D/775' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3C=COC3=C2)CC1)

`REAL300025051882.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051882.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051882/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051882 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3C=COC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 19, 57, 66, 120, 120, 120, 120, 120, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 57, 57, 120, 19, 5, 5, 3, 9, 9, 9, 9, 9, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 328
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051882 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3C=COC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 27, 13, 1, 1, 1, 1, 1, 1, 1, 55, 55, 100, 120, 120, 120, 120, 201, 201, 201, 201, 201, 201, 201, 201, 120, 120, 27, 27, 1, 55, 100, 100, 120, 201, 201, 201, 201, 201, 120, 120, 120, 120] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 577
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051882 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C3C=COC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 148, 157, 201, 201, 201, 201, 201, 17, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 148, 148, 201, 62, 17, 17, 5, 1, 1, 1, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42])
total number of confs: 683
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051882 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051882
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051882/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051882
Building REAL300025051883
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051883'
/scratch/stefan/7786831/working/building/REAL300025051883 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051883

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051883/0 /scratch/stefan/7786831/working/building/REAL300025051883 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 776)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/776
`/scratch/stefan/7786831/working/3D/776' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051883.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051883.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051883/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051883 none NC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 28, 28, 28, 87, 105, 201, 201, 201, 201, 201, 1, 1, 4, 4, 4, 4, 2, 7, 7, 28, 87, 87, 201, 1, 1, 1, 1, 4] 201
rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38])
total number of confs: 533
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051883 none NC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 13, 43, 43, 43, 105, 124, 201, 201, 201, 201, 201, 4, 4, 1, 2, 2, 1, 4, 13, 13, 43, 105, 105, 201, 4, 4, 4, 4, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 23, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 573
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051883 none NC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 150, 56, 56, 29, 56, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 150, 150, 56, 29, 29, 1, 201, 201, 201, 201, 201] 201
rigid atoms, others: [33, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 764
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051883 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051883
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051883/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051883
Building REAL300025051884
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051884'
/scratch/stefan/7786831/working/building/REAL300025051884 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051884

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051884/0 /scratch/stefan/7786831/working/building/REAL300025051884 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 777)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/777
`/scratch/stefan/7786831/working/3D/777' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NOC(COCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1)

`REAL300025051884.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051884.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051884/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051884 none CC1=NOC(COCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 12, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [47, 47, 47, 47, 22, 11, 5, 2, 2, 2, 1, 1, 1, 3, 5, 5, 5, 13, 18, 46, 46, 46, 46, 46, 1, 1, 47, 47, 47, 47, 22, 22, 5, 5, 2, 3, 3, 5, 13, 13, 46, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 10, 11, 12, 44, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 208
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051884 none CC1=NOC(COCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 12, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 23, 30, 47, 47, 47, 47, 73, 86, 86, 86, 137, 165, 201, 201, 201, 201, 201, 47, 47, 1, 2, 2, 2, 9, 9, 30, 30, 47, 73, 73, 86, 137, 137, 201, 47, 47, 47, 47] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 727
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051884 none CC1=NOC(COCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 12, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 160, 123, 84, 46, 46, 46, 46, 43, 39, 39, 35, 39, 13, 1, 1, 1, 1, 1, 1, 1, 46, 46, 201, 201, 201, 201, 160, 160, 84, 84, 46, 43, 43, 39, 35, 35, 1, 46, 46, 46, 46] 201
rigid atoms, others: [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, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 696
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051884 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051884
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051884/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051884
Building REAL300025051885
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051885'
/scratch/stefan/7786831/working/building/REAL300025051885 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051885

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051885/0 /scratch/stefan/7786831/working/building/REAL300025051885 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 778)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/778
`/scratch/stefan/7786831/working/3D/778' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCSC2)CC1)

`REAL300025051885.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051885.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051885/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051885 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCSC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 25, 73, 85, 158, 158, 158, 158, 158, 6, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 1, 1, 73, 73, 158, 25, 6, 6, 3, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 434
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051885 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCSC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [76, 32, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 131, 158, 158, 158, 158, 201, 201, 201, 201, 158, 158, 32, 32, 1, 76, 131, 131, 158, 201, 201, 201, 201, 201, 201, 201, 158, 158, 158, 158] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 25] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 743
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051885 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCSC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [73, 73, 73, 153, 159, 201, 201, 201, 201, 201, 24, 14, 8, 8, 1, 8, 1, 1, 1, 1, 1, 14, 14, 153, 153, 201, 73, 24, 24, 8, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14] 201
rigid atoms, others: [32, 33, 34, 35, 36, 14, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40])
total number of confs: 705
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051885 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051885
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051885/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051885
Building REAL300025051886
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051886'
/scratch/stefan/7786831/working/building/REAL300025051886 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051886

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051886/0 /scratch/stefan/7786831/working/building/REAL300025051886 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 779)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/779
`/scratch/stefan/7786831/working/3D/779' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCO2)CC1)

`REAL300025051886.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051886.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051886/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051886 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 28, 28, 98, 117, 201, 201, 201, 201, 201, 6, 1, 1, 1, 3, 3, 3, 8, 8, 8, 1, 1, 98, 98, 201, 28, 6, 6, 3, 8, 8, 8, 8, 8, 1, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
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: REAL300025051886 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [78, 35, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 171, 201, 201, 201, 201, 201, 201, 201, 201, 201, 35, 35, 1, 78, 171, 171, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 760
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051886 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [52, 52, 52, 135, 148, 201, 201, 201, 201, 201, 15, 8, 5, 5, 1, 5, 1, 1, 1, 1, 8, 8, 135, 135, 201, 52, 15, 15, 5, 1, 1, 1, 1, 1, 8, 8, 8, 8] 201
rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37])
total number of confs: 623
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051886 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051886
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051886/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051886
Building REAL300025051887
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051887'
/scratch/stefan/7786831/working/building/REAL300025051887 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051887

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051887/0 /scratch/stefan/7786831/working/building/REAL300025051887 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 780)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/780
`/scratch/stefan/7786831/working/3D/780' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCNC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1)

`REAL300025051887.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051887.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051887/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051887 none CCNC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 9, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 3, 8, 8, 8, 17, 24, 100, 100, 100, 100, 100, 1, 1, 3, 3, 15, 15, 15, 15, 15, 9, 3, 3, 2, 3, 3, 8, 17, 17, 100, 1, 1, 1, 1, 3] 149
rigid atoms, others: [43, 9, 10, 11, 44, 45, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46])
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: REAL300025051887 none CCNC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 14, 14, 14, 27, 36, 107, 107, 107, 107, 107, 3, 3, 1, 1, 10, 10, 10, 10, 10, 5, 1, 1, 3, 5, 5, 14, 27, 27, 107, 3, 3, 3, 3, 1] 149
rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 46, 25, 26] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 257
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051887 none CCNC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
149  conformations in input
total number of sets (complete confs): 149
using faster count positions algorithm for large data
unique positions, atoms: [149, 144, 107, 107, 107, 107, 100, 100, 100, 100, 76, 59, 59, 34, 59, 13, 1, 1, 1, 1, 1, 1, 1, 100, 100, 107, 107, 149, 149, 149, 149, 149, 144, 107, 107, 100, 76, 76, 59, 34, 34, 1, 100, 100, 100, 100, 107] 149
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46])
total number of confs: 588
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051887 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051887
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051887/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051887
Building REAL300025051888
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051888'
/scratch/stefan/7786831/working/building/REAL300025051888 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051888

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051888/0 /scratch/stefan/7786831/working/building/REAL300025051888 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 781)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/781
`/scratch/stefan/7786831/working/3D/781' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=CC1CCCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051888.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051888.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051888/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051888 none O=C(C=CC1CCCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 8, 8, 18, 18, 18, 18, 18, 1, 1, 1, 4, 7, 7, 7, 24, 37, 106, 106, 106, 106, 106, 1, 1, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 4, 4, 7, 24, 24, 106, 1, 1, 1, 1] 201
rigid atoms, others: [10, 11, 12, 46, 47, 48, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 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: REAL300025051888 none O=C(C=CC1CCCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 3, 3, 1, 1, 1, 1, 1, 1, 1, 17, 18, 18, 36, 51, 51, 51, 115, 148, 201, 201, 201, 201, 201, 18, 18, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 36, 36, 51, 115, 115, 201, 18, 18, 18, 18] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 37, 35, 36, 38, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 662
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051888 none O=C(C=CC1CCCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [106, 106, 106, 200, 200, 201, 201, 201, 201, 201, 106, 95, 57, 57, 27, 57, 13, 1, 1, 1, 1, 1, 1, 1, 106, 106, 200, 200, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 106, 95, 95, 57, 27, 27, 1, 106, 106, 106, 106] 201
rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49])
total number of confs: 714
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051888 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051888
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051888/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051888
Building REAL300025051889
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051889'
/scratch/stefan/7786831/working/building/REAL300025051889 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051889

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051889/0 /scratch/stefan/7786831/working/building/REAL300025051889 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 782)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/782
`/scratch/stefan/7786831/working/3D/782' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(O)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051889.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051889.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051889/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051889 none CCCC(O)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 189, 176, 189, 102, 102, 102, 102, 86, 61, 61, 29, 61, 13, 1, 1, 1, 1, 1, 1, 1, 102, 102, 201, 201, 201, 201, 201, 201, 201, 189, 567, 176, 176, 102, 86, 86, 61, 29, 29, 1, 102, 102, 102, 102] 603
rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 1441
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051889 none CCCC(O)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 19, 9, 19, 2, 2, 2, 1, 1, 1, 4, 6, 6, 6, 20, 34, 102, 102, 102, 102, 102, 1, 1, 30, 30, 30, 30, 30, 30, 30, 19, 57, 9, 9, 2, 4, 4, 6, 20, 20, 102, 1, 1, 1, 1] 603
rigid atoms, others: [8, 9, 10, 43, 44, 45, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
total number of confs: 392
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051889 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051889
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051889/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051889
Building REAL300025051890
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051890'
/scratch/stefan/7786831/working/building/REAL300025051890 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051890

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051890/0 /scratch/stefan/7786831/working/building/REAL300025051890 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 783)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/783
`/scratch/stefan/7786831/working/3D/783' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CCCO2)CC1)

`REAL300025051890.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051890.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051890/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051890 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CCCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 97, 117, 198, 198, 198, 198, 198, 6, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 1, 1, 97, 97, 198, 28, 6, 6, 3, 9, 9, 9, 9, 9, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 531
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051890 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CCCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 33, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 161, 198, 198, 198, 198, 201, 201, 201, 201, 198, 198, 33, 33, 1, 74, 161, 161, 198, 201, 201, 201, 201, 201, 198, 198, 198, 198] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 25] set([0, 1, 2, 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: 745
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051890 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CCCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 115, 134, 201, 201, 201, 201, 201, 15, 9, 6, 6, 1, 6, 1, 1, 1, 1, 1, 9, 9, 115, 115, 201, 45, 15, 15, 6, 1, 1, 1, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38])
total number of confs: 571
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051890 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051890
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051890/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051890
Building REAL300025051891
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051891'
/scratch/stefan/7786831/working/building/REAL300025051891 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051891

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051891/0 /scratch/stefan/7786831/working/building/REAL300025051891 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 784)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/784
`/scratch/stefan/7786831/working/3D/784' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(CO)O2)CC1)

`REAL300025051891.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051891.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051891/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051891 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(CO)O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 12, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 18, 56, 63, 152, 152, 152, 152, 152, 5, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 35, 14, 1, 1, 56, 56, 152, 18, 5, 5, 3, 14, 14, 35, 35, 105, 1, 1, 1, 1] 603
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 555
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051891 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(CO)O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 12, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [62, 33, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 118, 152, 152, 152, 152, 200, 200, 200, 200, 201, 200, 152, 152, 33, 33, 1, 62, 118, 118, 152, 200, 200, 201, 201, 603, 152, 152, 152, 152] 603
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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])
total number of confs: 1280
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051891 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(CO)O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 12, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [60, 60, 60, 114, 124, 200, 200, 200, 200, 200, 22, 14, 9, 8, 1, 8, 1, 1, 1, 1, 1, 7, 1, 14, 14, 114, 114, 200, 60, 22, 22, 9, 1, 1, 7, 7, 21, 14, 14, 14, 14] 603
rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 622
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051891 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051891
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051891/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051891
Building REAL300025051892
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051892'
/scratch/stefan/7786831/working/building/REAL300025051892 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051892

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051892/0 /scratch/stefan/7786831/working/building/REAL300025051892 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 785)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/785
`/scratch/stefan/7786831/working/3D/785' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=C1O)

`REAL300025051892.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051892.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051892/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051892 none COC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 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]
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, 5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 14, 14, 14, 46, 57, 128, 128, 128, 128, 128, 1, 1, 5, 5, 5, 5, 11, 11, 11, 5, 2, 4, 4, 14, 46, 46, 128, 1, 1, 1, 1, 5, 5, 10] 402
rigid atoms, others: [38, 7, 8, 9, 39, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 42, 43, 44])
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: REAL300025051892 none COC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 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]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 36, 36, 36, 84, 100, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 1, 3, 3, 3, 1, 5, 12, 12, 36, 84, 84, 201, 5, 5, 5, 5, 1, 1, 2] 402
rigid atoms, others: [1, 2, 3, 4, 5, 42, 43, 23, 24, 25, 26, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44])
total number of confs: 522
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051892 none COC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 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]
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, 128, 128, 128, 128, 103, 66, 66, 32, 66, 13, 1, 1, 1, 1, 1, 1, 1, 128, 128, 201, 201, 201, 201, 201, 201, 201, 201, 128, 103, 103, 66, 32, 32, 1, 128, 128, 128, 128, 201, 201, 402] 402
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 1011
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051892 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051892
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051892/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051892
Building REAL300025051893
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051893'
/scratch/stefan/7786831/working/building/REAL300025051893 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051893

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051893/0 /scratch/stefan/7786831/working/building/REAL300025051893 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 786)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/786
`/scratch/stefan/7786831/working/3D/786' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(N)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051893.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051893.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051893/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051893 none COC1=CC=C(N)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 7, 17, 17, 17, 49, 60, 135, 135, 135, 135, 135, 1, 1, 9, 13, 13, 13, 9, 9, 9, 9, 2, 7, 7, 17, 49, 49, 135, 1, 1, 1, 1, 9] 201
rigid atoms, others: [43, 41, 10, 11, 12, 44, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45])
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: REAL300025051893 none COC1=CC=C(N)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 9, 9, 9, 9, 24, 41, 41, 41, 96, 109, 201, 201, 201, 201, 201, 9, 9, 1, 3, 3, 3, 1, 1, 2, 2, 9, 24, 24, 41, 96, 96, 201, 9, 9, 9, 9, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 45, 26, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 581
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051893 none COC1=CC=C(N)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 135, 135, 135, 135, 95, 56, 56, 26, 56, 12, 1, 1, 1, 1, 1, 1, 1, 135, 135, 201, 201, 201, 201, 201, 201, 201, 201, 135, 95, 95, 56, 26, 26, 1, 135, 135, 135, 135, 201] 201
rigid atoms, others: [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, 37, 38, 39, 41, 42, 43, 44, 45])
total number of confs: 618
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051893 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051893
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051893/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051893
Building REAL300025051894
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051894'
/scratch/stefan/7786831/working/building/REAL300025051894 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051894

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051894/0 /scratch/stefan/7786831/working/building/REAL300025051894 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 787)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/787
`/scratch/stefan/7786831/working/3D/787' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)=CCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051894.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051894.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051894/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051894 none CC(C)=CCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 200, 199, 121, 121, 121, 121, 103, 57, 57, 27, 57, 13, 1, 1, 1, 1, 1, 1, 1, 121, 121, 201, 201, 201, 201, 201, 201, 201, 200, 200, 199, 199, 121, 103, 103, 57, 27, 27, 1, 121, 121, 121, 121] 201
rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 858
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051894 none CC(C)=CCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 18, 17, 10, 2, 2, 2, 1, 1, 1, 4, 8, 8, 8, 25, 41, 121, 121, 121, 121, 121, 1, 1, 18, 18, 18, 18, 18, 18, 18, 17, 17, 10, 10, 2, 4, 4, 8, 25, 25, 121, 1, 1, 1, 1] 201
rigid atoms, others: [8, 9, 10, 43, 44, 45, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
total number of confs: 317
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051894 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051894
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051894/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051894
Building REAL300025051895
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051895'
/scratch/stefan/7786831/working/building/REAL300025051895 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051895

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051895/0 /scratch/stefan/7786831/working/building/REAL300025051895 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 788)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/788
`/scratch/stefan/7786831/working/3D/788' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(C=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)CC)

`REAL300025051895.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051895.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051895/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051895 none CC=C(C=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)CC NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [145, 145, 102, 102, 78, 78, 78, 78, 66, 41, 41, 21, 41, 12, 1, 1, 1, 1, 1, 1, 1, 78, 78, 145, 201, 145, 145, 145, 145, 102, 102, 78, 66, 66, 41, 21, 21, 1, 78, 78, 78, 78, 201, 201, 201, 201, 201] 201
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 876
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051895 none CC=C(C=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)CC NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 8, 8, 2, 2, 2, 1, 1, 1, 4, 6, 6, 6, 20, 30, 78, 78, 78, 78, 78, 1, 1, 18, 32, 18, 18, 18, 18, 8, 8, 2, 4, 4, 6, 20, 20, 78, 1, 1, 1, 1, 32, 32, 32, 32, 32] 201
rigid atoms, others: [38, 7, 8, 9, 39, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 42, 43, 44, 45, 46])
total number of confs: 294
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051895 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051895
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051895/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051895
Building REAL300025051896
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051896'
/scratch/stefan/7786831/working/building/REAL300025051896 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051896

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051896/0 /scratch/stefan/7786831/working/building/REAL300025051896 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 789)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/789
`/scratch/stefan/7786831/working/3D/789' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2COC2)CC1)

`REAL300025051896.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051896.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051896/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051896 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2COC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 34, 54, 119, 119, 119, 119, 119, 5, 1, 1, 1, 3, 3, 3, 23, 23, 23, 1, 1, 34, 34, 119, 11, 5, 5, 3, 23, 23, 23, 23, 23, 1, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 305
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: REAL300025051896 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2COC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [66, 44, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 111, 119, 119, 119, 119, 201, 201, 201, 119, 119, 44, 44, 1, 66, 111, 111, 119, 201, 201, 201, 201, 201, 119, 119, 119, 119] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 745
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051896 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2COC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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, 115, 144, 201, 201, 201, 201, 201, 32, 23, 13, 13, 1, 13, 1, 1, 1, 1, 23, 23, 115, 115, 201, 57, 32, 32, 13, 1, 1, 1, 1, 1, 23, 23, 23, 23] 201
rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37])
total number of confs: 625
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051896 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051896
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051896/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051896
Building REAL300025051897
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051897'
/scratch/stefan/7786831/working/building/REAL300025051897 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051897

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051897/0 /scratch/stefan/7786831/working/building/REAL300025051897 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 790)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/790
`/scratch/stefan/7786831/working/3D/790' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(N)=N1)

`REAL300025051897.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051897.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051897/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051897 none CC1=NC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(N)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [9, 4, 9, 9, 2, 2, 2, 1, 1, 1, 6, 20, 20, 20, 43, 51, 106, 106, 106, 106, 106, 1, 1, 9, 9, 9, 9, 9, 9, 9, 2, 6, 6, 20, 43, 43, 106, 1, 1, 1, 1, 9, 9] 201
rigid atoms, others: [37, 38, 7, 8, 9, 39, 40, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 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, 41, 42])
total number of confs: 291
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051897 none CC1=NC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(N)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 25, 60, 60, 60, 108, 117, 201, 201, 201, 201, 201, 9, 9, 1, 1, 1, 2, 2, 2, 1, 9, 25, 25, 60, 108, 108, 201, 9, 9, 9, 9, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 23, 24, 25, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 589
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051897 none CC1=NC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(N)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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, 193, 201, 201, 106, 106, 106, 106, 71, 38, 38, 24, 38, 13, 1, 1, 1, 1, 1, 1, 1, 106, 106, 201, 201, 201, 201, 201, 201, 201, 106, 71, 71, 38, 24, 24, 1, 106, 106, 106, 106, 201, 201] 201
rigid atoms, others: [36, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42])
total number of confs: 600
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051897 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051897
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051897/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051897
Building REAL300025051898
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051898'
/scratch/stefan/7786831/working/building/REAL300025051898 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051898

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051898/0 /scratch/stefan/7786831/working/building/REAL300025051898 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 791)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/791
`/scratch/stefan/7786831/working/3D/791' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=CC1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051898.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051898.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051898/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051898 none O=C(C=CC1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 9, 9, 19, 19, 19, 19, 1, 1, 1, 4, 7, 7, 7, 27, 39, 121, 121, 121, 121, 121, 1, 1, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 4, 4, 7, 27, 27, 121, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 46, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 291
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051898 none O=C(C=CC1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 5, 5, 1, 1, 1, 1, 1, 1, 19, 19, 19, 34, 48, 48, 48, 112, 144, 201, 201, 201, 201, 201, 19, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 34, 34, 48, 112, 112, 201, 19, 19, 19, 19] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 35, 27, 28, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 633
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051898 none O=C(C=CC1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [121, 121, 121, 199, 199, 201, 201, 201, 201, 121, 103, 61, 61, 28, 61, 13, 1, 1, 1, 1, 1, 1, 1, 121, 121, 199, 199, 201, 201, 201, 201, 201, 201, 201, 201, 201, 121, 103, 103, 61, 28, 28, 1, 121, 121, 121, 121] 201
rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46])
total number of confs: 747
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051898 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051898
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051898/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051898
Building REAL300025051899
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051899'
/scratch/stefan/7786831/working/building/REAL300025051899 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051899

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051899/0 /scratch/stefan/7786831/working/building/REAL300025051899 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 792)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/792
`/scratch/stefan/7786831/working/3D/792' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(CO)C(F)=C2)CC1)

`REAL300025051899.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051899.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051899/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051899 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(CO)C(F)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 12, 1, 15, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 12, 40, 47, 112, 112, 112, 112, 112, 4, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 21, 9, 9, 9, 1, 1, 40, 40, 112, 12, 4, 4, 3, 9, 9, 21, 21, 63, 9, 1, 1, 1, 1] 603
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
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: REAL300025051899 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(CO)C(F)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 12, 1, 15, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [67, 31, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 103, 112, 112, 112, 112, 201, 201, 201, 201, 201, 201, 201, 201, 112, 112, 31, 31, 1, 67, 103, 103, 112, 201, 201, 201, 201, 603, 201, 112, 112, 112, 112] 603
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 1157
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051899 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(CO)C(F)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 12, 1, 15, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [41, 41, 41, 110, 121, 201, 201, 201, 201, 201, 13, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 5, 1, 1, 1, 9, 9, 110, 110, 201, 41, 13, 13, 5, 1, 1, 5, 5, 15, 1, 9, 9, 9, 9] 603
rigid atoms, others: [34, 35, 39, 14, 16, 17, 18, 19, 20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 623
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051899 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051899
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051899/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051899
Building REAL300025051900
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051900'
/scratch/stefan/7786831/working/building/REAL300025051900 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051900

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051900/0 /scratch/stefan/7786831/working/building/REAL300025051900 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 793)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/793
`/scratch/stefan/7786831/working/3D/793' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCC(=O)C2)CC1)

`REAL300025051900.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051900.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051900/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051900 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCC(=O)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 18, 24, 74, 74, 74, 74, 74, 5, 1, 1, 1, 3, 3, 3, 19, 43, 43, 43, 43, 43, 1, 1, 18, 18, 74, 10, 5, 5, 3, 19, 19, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 42, 11, 12, 13, 44, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 288
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051900 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCC(=O)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 13, 1, 1, 1, 1, 1, 1, 1, 51, 51, 72, 74, 74, 74, 74, 187, 201, 201, 201, 201, 201, 74, 74, 34, 34, 1, 51, 72, 72, 74, 187, 187, 201, 201, 201, 201, 201, 201, 201, 74, 74, 74, 74] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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: 798
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051900 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCC(=O)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [90, 90, 90, 124, 145, 201, 201, 201, 201, 201, 46, 43, 29, 29, 6, 29, 1, 1, 1, 1, 1, 1, 1, 43, 43, 124, 124, 201, 90, 46, 46, 29, 6, 6, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44])
total number of confs: 638
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051900 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051900
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051900/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051900
Building REAL300025051901
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051901'
/scratch/stefan/7786831/working/building/REAL300025051901 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051901

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051901/0 /scratch/stefan/7786831/working/building/REAL300025051901 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 794)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/794
`/scratch/stefan/7786831/working/3D/794' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C23CCC(F)(CC2)CC3)CC1)

`REAL300025051901.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051901.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051901/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051901 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C23CCC(F)(CC2)CC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 25, 85, 98, 145, 145, 145, 145, 145, 6, 1, 1, 1, 3, 3, 3, 8, 8, 3, 3, 8, 8, 8, 8, 1, 1, 85, 85, 145, 25, 6, 6, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1] 146
rigid atoms, others: [11, 12, 13, 46, 47, 48, 49, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
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: REAL300025051901 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C23CCC(F)(CC2)CC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [85, 37, 13, 1, 1, 1, 1, 1, 1, 1, 85, 85, 133, 145, 145, 145, 145, 146, 146, 145, 145, 146, 146, 146, 146, 145, 145, 37, 37, 1, 85, 133, 133, 145, 146, 146, 146, 146, 146, 146, 146, 146, 146, 146, 146, 146, 145, 145, 145, 145] 146
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46, 47, 48, 49])
total number of confs: 547
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051901 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C23CCC(F)(CC2)CC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [43, 43, 43, 99, 108, 146, 146, 146, 146, 146, 14, 8, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 99, 99, 146, 43, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 146
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 46, 47, 48, 49])
total number of confs: 458
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051901 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051901
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051901/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051901
Building REAL300025051902
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051902'
/scratch/stefan/7786831/working/building/REAL300025051902 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051902

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051902/0 /scratch/stefan/7786831/working/building/REAL300025051902 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 795)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/795
`/scratch/stefan/7786831/working/3D/795' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCC1)

`REAL300025051902.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051902.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051902/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051902 none N#CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCC1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
164  conformations in input
total number of sets (complete confs): 164
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 2, 2, 2, 1, 1, 1, 6, 20, 20, 20, 60, 79, 136, 136, 136, 136, 136, 1, 1, 11, 11, 11, 2, 6, 6, 20, 60, 60, 136, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11] 164
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 20, 21] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41])
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: REAL300025051902 none N#CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCC1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 10, 10, 11, 11, 26, 56, 56, 56, 108, 133, 164, 164, 164, 164, 164, 11, 11, 1, 1, 1, 11, 26, 26, 56, 108, 108, 164, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1] 164
rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 39, 40, 41, 22, 23, 24, 36] set([5, 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: 543
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051902 none N#CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCC1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 136, 136, 136, 136, 115, 70, 70, 28, 70, 13, 1, 1, 1, 1, 1, 1, 1, 136, 136, 164, 164, 164, 136, 115, 115, 70, 28, 28, 1, 136, 136, 136, 136, 164, 164, 164, 164, 164, 164] 164
rigid atoms, others: [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, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 547
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051902 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051902
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051902/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051902
Building REAL300025051903
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051903'
/scratch/stefan/7786831/working/building/REAL300025051903 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051903

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051903/0 /scratch/stefan/7786831/working/building/REAL300025051903 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 796)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/796
`/scratch/stefan/7786831/working/3D/796' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C(C3CC3)N2)CC1)

`REAL300025051903.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051903.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051903/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051903 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C(C3CC3)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', '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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
142  conformations in input
total number of sets (complete confs): 142
using faster count positions algorithm for large data
unique positions, atoms: [14, 14, 14, 36, 43, 80, 80, 80, 80, 80, 5, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 43, 43, 10, 1, 1, 36, 36, 80, 14, 5, 5, 3, 10, 43, 43, 43, 43, 43, 10, 1, 1, 1, 1] 142
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 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: REAL300025051903 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C(C3CC3)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', '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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
142  conformations in input
total number of sets (complete confs): 142
using faster count positions algorithm for large data
unique positions, atoms: [48, 26, 13, 1, 1, 1, 1, 1, 1, 1, 48, 48, 67, 80, 80, 80, 80, 93, 93, 93, 93, 142, 142, 93, 80, 80, 26, 26, 1, 48, 67, 67, 80, 93, 142, 142, 142, 142, 142, 93, 80, 80, 80, 80] 142
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 532
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051903 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C(C3CC3)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', '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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
142  conformations in input
total number of sets (complete confs): 142
using faster count positions algorithm for large data
unique positions, atoms: [104, 104, 104, 132, 135, 142, 142, 142, 142, 142, 65, 43, 34, 34, 13, 34, 13, 13, 13, 1, 1, 1, 1, 13, 43, 43, 132, 132, 142, 104, 65, 65, 34, 13, 1, 1, 1, 1, 1, 13, 43, 43, 43, 43] 142
rigid atoms, others: [34, 35, 36, 37, 38, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43])
total number of confs: 551
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051903 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C(C3CC3)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', '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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
142  conformations in input
total number of sets (complete confs): 142
using faster count positions algorithm for large data
unique positions, atoms: [34, 34, 34, 63, 68, 93, 93, 93, 93, 93, 15, 10, 7, 7, 1, 7, 1, 1, 1, 1, 1, 13, 13, 1, 10, 10, 63, 63, 93, 34, 15, 15, 7, 1, 13, 13, 13, 13, 13, 1, 10, 10, 10, 10] 142
rigid atoms, others: [33, 39, 14, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 331
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051903 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051903
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051903/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051903
Building REAL300025051904
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051904'
/scratch/stefan/7786831/working/building/REAL300025051904 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051904

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051904/0 /scratch/stefan/7786831/working/building/REAL300025051904 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 797)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/797
`/scratch/stefan/7786831/working/3D/797' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1)

`REAL300025051904.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051904.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051904/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051904 none CC1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 7, 25, 25, 25, 70, 81, 181, 181, 181, 181, 181, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 7, 7, 25, 70, 70, 181, 1, 1, 1, 1] 201
rigid atoms, others: [7, 8, 9, 42, 43, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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])
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051904 none CC1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 25, 65, 65, 65, 131, 140, 201, 201, 201, 201, 201, 7, 7, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 25, 25, 65, 131, 131, 201, 7, 7, 7, 7] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 23, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 663
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051904 none CC1CCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 181, 181, 181, 181, 123, 43, 43, 25, 43, 12, 1, 1, 1, 1, 1, 1, 1, 181, 181, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 181, 123, 123, 43, 25, 25, 1, 181, 181, 181, 181] 201
rigid atoms, others: [39, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 750
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051904 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051904
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051904/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051904
Building REAL300025051905
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051905'
/scratch/stefan/7786831/working/building/REAL300025051905 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051905

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051905/0 /scratch/stefan/7786831/working/building/REAL300025051905 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 798)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/798
`/scratch/stefan/7786831/working/3D/798' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNC1=NC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1)

`REAL300025051905.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051905.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051905/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051905 none CNC1=NC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 25, 25, 25, 88, 110, 201, 201, 201, 201, 201, 1, 1, 4, 5, 5, 5, 5, 4, 2, 7, 7, 25, 88, 88, 201, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 40, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 533
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051905 none CNC1=NC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 28, 28, 28, 91, 111, 201, 201, 201, 201, 201, 4, 4, 1, 3, 3, 3, 2, 1, 4, 10, 10, 28, 91, 91, 201, 4, 4, 4, 4] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 24, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 538
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051905 none CNC1=NC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 151, 68, 68, 30, 68, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 151, 151, 68, 30, 30, 1, 201, 201, 201, 201] 201
rigid atoms, others: [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, 34, 35, 37, 38, 39, 40])
total number of confs: 765
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051905 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051905
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051905/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051905
Building REAL300025051906
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051906'
/scratch/stefan/7786831/working/building/REAL300025051906 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051906

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051906/0 /scratch/stefan/7786831/working/building/REAL300025051906 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 799)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/799
`/scratch/stefan/7786831/working/3D/799' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C(F)C(F)=C2)CC1)

`REAL300025051906.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051906.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051906/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051906 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C(F)C(F)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 15, 1, 15, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 25, 70, 79, 121, 121, 121, 121, 121, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 1, 1, 70, 70, 121, 25, 5, 5, 3, 9, 9, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34])
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: REAL300025051906 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C(F)C(F)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 15, 1, 15, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [59, 29, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 93, 121, 121, 121, 121, 201, 201, 201, 201, 201, 201, 201, 121, 121, 29, 29, 1, 59, 93, 93, 121, 201, 201, 121, 121, 121, 121] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 571
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051906 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C(F)C(F)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 15, 1, 15, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [69, 69, 69, 156, 170, 201, 201, 201, 201, 201, 15, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 156, 156, 201, 69, 15, 15, 5, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [33, 34, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38])
total number of confs: 676
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051906 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051906
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051906/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051906
Building REAL300025051907
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051907'
/scratch/stefan/7786831/working/building/REAL300025051907 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051907

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051907/0 /scratch/stefan/7786831/working/building/REAL300025051907 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 800)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/800
`/scratch/stefan/7786831/working/3D/800' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=NC(F)=C2F)CC1)

`REAL300025051907.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051907.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051907/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051907 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=NC(F)=C2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 15, 1, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 27, 91, 100, 195, 195, 195, 195, 195, 7, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 1, 1, 91, 91, 195, 27, 7, 7, 3, 10, 10, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 508
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051907 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=NC(F)=C2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 15, 1, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [70, 37, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 145, 195, 195, 195, 195, 201, 201, 201, 201, 201, 201, 201, 195, 195, 37, 37, 1, 70, 145, 145, 195, 201, 201, 195, 195, 195, 195] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 731
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051907 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=NC(F)=C2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 15, 1, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [54, 54, 54, 142, 149, 201, 201, 201, 201, 201, 18, 10, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 142, 142, 201, 54, 18, 18, 7, 1, 1, 10, 10, 10, 10] 201
rigid atoms, others: [33, 34, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38])
total number of confs: 654
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051907 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051907
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051907/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051907
Building REAL300025051908
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051908'
/scratch/stefan/7786831/working/building/REAL300025051908 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051908

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051908/0 /scratch/stefan/7786831/working/building/REAL300025051908 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 801)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/801
`/scratch/stefan/7786831/working/3D/801' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=CNN=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051908.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051908.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051908/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051908 none NC1=CNN=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 6, 25, 25, 25, 110, 133, 199, 199, 199, 199, 199, 1, 1, 4, 4, 4, 4, 2, 6, 6, 25, 110, 110, 199, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
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: REAL300025051908 none NC1=CNN=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 12, 36, 36, 36, 123, 143, 201, 201, 201, 201, 201, 4, 4, 1, 1, 1, 1, 4, 12, 12, 36, 123, 123, 201, 4, 4, 4, 4] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 583
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051908 none NC1=CNN=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 199, 199, 199, 199, 171, 77, 77, 30, 77, 13, 1, 1, 1, 1, 1, 1, 1, 199, 199, 201, 201, 201, 201, 199, 171, 171, 77, 30, 30, 1, 199, 199, 199, 199] 201
rigid atoms, others: [34, 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, 35, 36, 37, 38])
total number of confs: 734
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051908 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051908/1 /scratch/stefan/7786831/working/building/REAL300025051908 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 802)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/802
`/scratch/stefan/7786831/working/3D/802' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)NN=C1)

`REAL300025051908.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051908.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051908/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051908 none NC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)NN=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 1, 6, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 2, 2, 2, 1, 1, 1, 4, 21, 21, 21, 52, 55, 78, 78, 78, 78, 78, 1, 1, 6, 6, 6, 6, 6, 2, 4, 4, 21, 52, 52, 78, 1, 1, 1, 1, 6, 6] 97
rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 19, 20] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38])
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: REAL300025051908 none NC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)NN=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 1, 6, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
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, 5, 5, 6, 6, 13, 39, 39, 39, 74, 76, 97, 97, 97, 97, 97, 6, 6, 1, 1, 1, 2, 2, 6, 13, 13, 39, 74, 74, 97, 6, 6, 6, 6, 1, 1] 97
rigid atoms, others: [0, 1, 2, 3, 37, 38, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 333
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051908 none NC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)NN=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 1, 6, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [97, 97, 78, 78, 78, 78, 72, 41, 41, 25, 41, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 97, 97, 97, 97, 97, 78, 72, 72, 41, 25, 25, 1, 78, 78, 78, 78, 97, 97] 97
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38])
total number of confs: 318
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051908 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051908
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051908/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051908/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051908
Building REAL300025051909
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051909'
/scratch/stefan/7786831/working/building/REAL300025051909 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051909

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051909/0 /scratch/stefan/7786831/working/building/REAL300025051909 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 803)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/803
`/scratch/stefan/7786831/working/3D/803' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(COC1=CC=C(O)C=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051909.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051909.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051909/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051909 none O=C(COC1=CC=C(O)C=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 2, 2, 5, 13, 17, 17, 13, 13, 17, 17, 1, 1, 1, 5, 14, 14, 14, 39, 53, 137, 137, 137, 137, 137, 1, 1, 5, 5, 17, 17, 34, 17, 17, 2, 5, 5, 14, 39, 39, 137, 1, 1, 1, 1] 402
rigid atoms, others: [43, 41, 42, 11, 12, 13, 44, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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])
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051909 none O=C(COC1=CC=C(O)C=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [17, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 32, 61, 61, 61, 106, 130, 201, 201, 201, 201, 201, 17, 17, 8, 8, 1, 1, 2, 1, 1, 17, 32, 32, 61, 106, 106, 201, 17, 17, 17, 17] 402
rigid atoms, others: [32, 33, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 598
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051909 none O=C(COC1=CC=C(O)C=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [137, 137, 137, 154, 201, 201, 201, 201, 201, 201, 201, 137, 113, 85, 85, 48, 85, 13, 1, 1, 1, 1, 1, 1, 1, 137, 137, 154, 154, 201, 201, 402, 201, 201, 137, 113, 113, 85, 48, 48, 1, 137, 137, 137, 137] 402
rigid atoms, others: [40, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 1114
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051909 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051909
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051909/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051909
Building REAL300025051910
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051910'
/scratch/stefan/7786831/working/building/REAL300025051910 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051910

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051910/0 /scratch/stefan/7786831/working/building/REAL300025051910 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 804)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/804
`/scratch/stefan/7786831/working/3D/804' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C=CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCOCC1)

`REAL300025051910.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051910.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051910/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051910 none CC1(C=CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 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, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 2, 2, 2, 1, 1, 1, 4, 7, 7, 7, 19, 31, 74, 74, 74, 74, 74, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 9, 9, 2, 4, 4, 7, 19, 19, 74, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20] 201
rigid atoms, others: [6, 39, 8, 41, 42, 7, 40, 20, 21] set([0, 1, 2, 3, 4, 5, 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, 36, 37, 38, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 216
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051910 none CC1(C=CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 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, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 4, 4, 20, 20, 20, 20, 39, 52, 52, 52, 104, 139, 201, 201, 201, 201, 201, 20, 20, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 20, 39, 39, 52, 104, 104, 201, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 43, 44, 45, 46, 47, 48, 49, 50, 22, 23, 24, 25, 26] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 651
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051910 none CC1(C=CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 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, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 132, 132, 74, 74, 74, 74, 70, 44, 44, 27, 44, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 201, 201, 201, 201, 201, 201, 201, 201, 132, 132, 74, 70, 70, 44, 27, 27, 1, 74, 74, 74, 74, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [38, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 730
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051910 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051910
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051910/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051910
Building REAL300025051911
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051911'
/scratch/stefan/7786831/working/building/REAL300025051911 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051911

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051911/0 /scratch/stefan/7786831/working/building/REAL300025051911 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 805)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/805
`/scratch/stefan/7786831/working/3D/805' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCOC3(CCC3)C2)CC1)

`REAL300025051911.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051911.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051911/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051911 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCOC3(CCC3)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 58, 73, 144, 144, 144, 144, 144, 5, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 58, 58, 144, 18, 5, 5, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 47, 48, 49, 50, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 382
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051911 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCOC3(CCC3)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 29, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 123, 144, 144, 144, 144, 201, 201, 201, 201, 201, 201, 201, 201, 144, 144, 29, 29, 1, 69, 123, 123, 144, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 144, 144, 144, 144] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46, 47, 48, 49, 50])
total number of confs: 744
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051911 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCOC3(CCC3)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 138, 153, 201, 201, 201, 201, 201, 21, 15, 9, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 138, 138, 201, 63, 21, 21, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15] 201
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 47, 48, 49, 50])
total number of confs: 677
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051911 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051911
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051911/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051911
Building REAL300025051912
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051912'
/scratch/stefan/7786831/working/building/REAL300025051912 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051912

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051912/0 /scratch/stefan/7786831/working/building/REAL300025051912 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 806)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/806
`/scratch/stefan/7786831/working/3D/806' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051912.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051912.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051912/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051912 none CC(C)(C)OC(=O)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 147, 201, 101, 101, 101, 101, 85, 59, 59, 23, 59, 13, 1, 1, 1, 1, 1, 1, 1, 101, 101, 201, 201, 201, 201, 201, 201, 201, 201, 201, 147, 147, 101, 85, 85, 59, 23, 23, 1, 101, 101, 101, 101] 201
rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47])
total number of confs: 787
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051912 none CC(C)(C)OC(=O)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 30, 30, 28, 6, 28, 2, 2, 2, 1, 1, 1, 4, 7, 7, 7, 22, 35, 101, 101, 101, 101, 101, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 6, 6, 2, 4, 4, 7, 22, 22, 101, 1, 1, 1, 1] 201
rigid atoms, others: [44, 10, 11, 12, 45, 46, 47, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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/7786831/working/building/REAL300025051912 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051912
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051912/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051912
Building REAL300025051913
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051913'
/scratch/stefan/7786831/working/building/REAL300025051913 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051913

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051913/0 /scratch/stefan/7786831/working/building/REAL300025051913 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 807)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/807
`/scratch/stefan/7786831/working/3D/807' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC([N+](=O)[O-])=NN2)CC1)

`REAL300025051913.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051913.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051913/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051913 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC([N+](=O)[O-])=NN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 11, 11, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 4, 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: [21, 21, 21, 57, 66, 94, 94, 94, 94, 94, 5, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 1, 1, 57, 57, 94, 21, 5, 5, 3, 10, 10, 1, 1, 1, 1] 100
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34])
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: REAL300025051913 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC([N+](=O)[O-])=NN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 11, 11, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 4, 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: [42, 24, 13, 1, 1, 1, 1, 1, 1, 1, 42, 42, 73, 94, 94, 94, 94, 100, 100, 100, 100, 100, 100, 100, 94, 94, 24, 24, 1, 42, 73, 73, 94, 100, 100, 94, 94, 94, 94] 100
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 349
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051913 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC([N+](=O)[O-])=NN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 11, 11, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 4, 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: [40, 40, 40, 80, 84, 100, 100, 100, 100, 100, 14, 10, 7, 6, 1, 6, 1, 1, 1, 1, 2, 2, 1, 1, 10, 10, 80, 80, 100, 40, 14, 14, 7, 1, 1, 10, 10, 10, 10] 100
rigid atoms, others: [33, 34, 14, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38])
total number of confs: 367
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051913 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051913
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051913/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051913
Building REAL300025051914
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051914'
/scratch/stefan/7786831/working/building/REAL300025051914 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051914

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051914/0 /scratch/stefan/7786831/working/building/REAL300025051914 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 808)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/808
`/scratch/stefan/7786831/working/3D/808' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=CCO)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051914.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051914.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051914/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051914 none O=C(C=CCO)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 12, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [162, 162, 162, 201, 201, 201, 162, 144, 88, 88, 31, 88, 13, 1, 1, 1, 1, 1, 1, 1, 162, 162, 201, 201, 201, 201, 603, 162, 144, 144, 88, 31, 31, 1, 162, 162, 162, 162] 603
rigid atoms, others: [33, 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, 34, 35, 36, 37])
total number of confs: 1382
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051914 none O=C(C=CCO)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 12, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 8, 8, 28, 1, 1, 1, 4, 7, 7, 7, 27, 51, 162, 162, 162, 162, 162, 1, 1, 8, 8, 28, 28, 84, 2, 4, 4, 7, 27, 27, 162, 1, 1, 1, 1] 603
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 20, 21] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 474
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051914 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051914
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051914/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051914
Building REAL300025051915
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051915'
/scratch/stefan/7786831/working/building/REAL300025051915 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051915

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051915/0 /scratch/stefan/7786831/working/building/REAL300025051915 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 809)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/809
`/scratch/stefan/7786831/working/3D/809' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCC3=NC=NN32)CC1)

`REAL300025051915.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051915.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051915/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051915 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCC3=NC=NN32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 1, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 19, 68, 83, 179, 179, 179, 179, 179, 6, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 68, 68, 179, 19, 6, 6, 3, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 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: REAL300025051915 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCC3=NC=NN32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 1, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [72, 33, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 148, 179, 179, 179, 179, 201, 201, 201, 201, 201, 201, 201, 201, 179, 179, 33, 33, 1, 72, 148, 148, 179, 201, 201, 201, 201, 201, 201, 201, 201, 179, 179, 179, 179] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45])
total number of confs: 766
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051915 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCC3=NC=NN32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 1, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 120, 135, 201, 201, 201, 201, 201, 18, 10, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 120, 120, 201, 52, 18, 18, 8, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44, 45])
total number of confs: 610
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051915 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051915
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051915/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051915
Building REAL300025051916
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051916'
/scratch/stefan/7786831/working/building/REAL300025051916 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051916

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051916/0 /scratch/stefan/7786831/working/building/REAL300025051916 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 810)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/810
`/scratch/stefan/7786831/working/3D/810' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1)

`REAL300025051916.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051916.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051916/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051916 none COC1=CC=CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 6, 22, 22, 22, 67, 74, 154, 154, 154, 154, 154, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 6, 6, 22, 67, 67, 154, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 404
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051916 none COC1=CC=CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 3, 9, 9, 9, 9, 14, 47, 47, 47, 103, 109, 201, 201, 201, 201, 201, 9, 9, 1, 2, 2, 2, 1, 1, 1, 3, 3, 9, 14, 14, 47, 103, 103, 201, 9, 9, 9, 9] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 26, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 559
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051916 none COC1=CC=CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 154, 154, 154, 154, 124, 63, 63, 31, 63, 13, 1, 1, 1, 1, 1, 1, 1, 154, 154, 201, 201, 201, 201, 201, 201, 201, 201, 201, 154, 124, 124, 63, 31, 31, 1, 154, 154, 154, 154] 201
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 844
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051916 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051916
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051916/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051916
Building REAL300025051917
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051917'
/scratch/stefan/7786831/working/building/REAL300025051917 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051917

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051917/0 /scratch/stefan/7786831/working/building/REAL300025051917 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 811)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/811
`/scratch/stefan/7786831/working/3D/811' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(O)C1=O)

`REAL300025051917.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051917.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051917/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051917 none CN1C=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(O)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 12, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 6, 2, 2, 2, 1, 1, 1, 7, 26, 26, 26, 73, 83, 184, 184, 184, 184, 184, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 7, 7, 26, 73, 73, 184, 1, 1, 1, 1, 18] 603
rigid atoms, others: [39, 8, 9, 42, 7, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 43])
total number of confs: 485
number of broken/clashed sets: 272
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051917 none CN1C=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(O)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 12, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 21, 63, 63, 63, 129, 139, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 2, 2, 2, 1, 1, 6, 21, 21, 63, 129, 129, 201, 6, 6, 6, 6, 3] 603
rigid atoms, others: [0, 1, 2, 3, 4, 5, 23, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 643
number of broken/clashed sets: 272
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051917 none CN1C=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C(O)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 12, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 184, 184, 184, 184, 114, 42, 42, 21, 42, 11, 1, 1, 1, 1, 1, 1, 1, 184, 184, 201, 201, 201, 201, 201, 201, 201, 201, 201, 184, 114, 114, 42, 21, 21, 1, 184, 184, 184, 184, 603] 603
rigid atoms, others: [38, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43])
total number of confs: 1304
number of broken/clashed sets: 272
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051917 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051917
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051917/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051917
Building REAL300025051918
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051918'
/scratch/stefan/7786831/working/building/REAL300025051918 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051918

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051918/0 /scratch/stefan/7786831/working/building/REAL300025051918 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 812)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/812
`/scratch/stefan/7786831/working/3D/812' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1)

`REAL300025051918.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051918.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051918/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051918 none CC(C)(C)C1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 3, 7, 7, 3, 3, 3, 2, 2, 2, 1, 1, 1, 7, 25, 25, 25, 67, 71, 198, 200, 200, 200, 200, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 2, 7, 7, 25, 67, 67, 200, 1, 1, 1, 1] 201
rigid atoms, others: [44, 10, 11, 12, 45, 46, 47, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
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: REAL300025051918 none CC(C)(C)C1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 2, 2, 3, 3, 9, 28, 28, 28, 71, 75, 199, 201, 201, 201, 201, 3, 3, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 3, 9, 9, 28, 71, 71, 201, 3, 3, 3, 3] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 36, 26] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 486
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051918 none CC(C)(C)C1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 200, 200, 200, 200, 106, 41, 41, 23, 41, 13, 1, 1, 1, 1, 1, 1, 1, 200, 200, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 106, 106, 41, 23, 23, 1, 200, 200, 200, 200] 201
rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47])
total number of confs: 697
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051918 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051918/1 /scratch/stefan/7786831/working/building/REAL300025051918 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 813)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/813
`/scratch/stefan/7786831/working/3D/813' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1=NN=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N1)

`REAL300025051918.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051918.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051918/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051918 none CC(C)(C)C1=NN=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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: [7, 3, 7, 7, 3, 3, 3, 2, 2, 2, 1, 1, 1, 7, 26, 26, 26, 63, 85, 199, 199, 199, 199, 199, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 7, 7, 26, 63, 63, 199, 1, 1, 1, 1, 3] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47])
total number of confs: 461
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051918 none CC(C)(C)C1=NN=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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: [4, 1, 4, 4, 1, 1, 1, 1, 1, 2, 2, 3, 3, 9, 32, 32, 32, 75, 98, 201, 201, 201, 201, 201, 3, 3, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 9, 9, 32, 75, 75, 201, 3, 3, 3, 3, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 47, 26] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 492
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051918 none CC(C)(C)C1=NN=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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, 199, 199, 199, 199, 141, 68, 68, 31, 68, 13, 1, 1, 1, 1, 1, 1, 1, 199, 199, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 199, 141, 141, 68, 31, 31, 1, 199, 199, 199, 199, 201] 201
rigid atoms, others: [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, 40, 41, 43, 44, 45, 46, 47])
total number of confs: 750
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051918 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051918
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051918/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051918/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051918
Building REAL300025051919
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051919'
/scratch/stefan/7786831/working/building/REAL300025051919 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051919

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051919/0 /scratch/stefan/7786831/working/building/REAL300025051919 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 814)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/814
`/scratch/stefan/7786831/working/3D/814' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1N)

`REAL300025051919.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051919.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051919/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051919 none NC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1N NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.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: [8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 6, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 6]
dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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: [7, 7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 7, 21, 21, 21, 56, 67, 130, 130, 130, 130, 130, 1, 1, 7, 7, 7, 7, 7, 7, 7, 2, 7, 7, 21, 56, 56, 130, 1, 1, 1, 1, 7, 7] 201
rigid atoms, others: [38, 39, 8, 9, 10, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 42, 43])
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: REAL300025051919 none NC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1N NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.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: [8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 6, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 6]
dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 26, 62, 62, 62, 116, 129, 201, 201, 201, 201, 201, 7, 7, 1, 1, 2, 2, 1, 1, 1, 7, 26, 26, 62, 116, 116, 201, 7, 7, 7, 7, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 25, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 607
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051919 none NC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1N NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.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: [8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 6, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 6]
dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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, 130, 130, 130, 130, 93, 50, 50, 25, 50, 13, 1, 1, 1, 1, 1, 1, 1, 130, 130, 201, 201, 201, 201, 201, 201, 201, 130, 93, 93, 50, 25, 25, 1, 130, 130, 130, 130, 201, 201] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43])
total number of confs: 589
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051919 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051919
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051919/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051919
Building REAL300025051920
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051920'
/scratch/stefan/7786831/working/building/REAL300025051920 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051920

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051920/0 /scratch/stefan/7786831/working/building/REAL300025051920 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 815)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/815
`/scratch/stefan/7786831/working/3D/815' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CNC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051920.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051920.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051920/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051920 none CCC1=CNC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 6, 6, 6, 6, 6, 2, 2, 2, 1, 1, 1, 6, 10, 10, 10, 38, 61, 148, 148, 148, 148, 148, 1, 1, 10, 10, 10, 10, 10, 6, 6, 6, 2, 6, 6, 10, 38, 38, 148, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
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: REAL300025051920 none CCC1=CNC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 14, 23, 23, 23, 62, 88, 160, 160, 160, 160, 160, 6, 6, 4, 4, 4, 4, 4, 1, 1, 1, 6, 14, 14, 23, 62, 62, 160, 6, 6, 6, 6] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 427
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051920 none CCC1=CNC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 160, 160, 160, 160, 160, 148, 148, 148, 148, 112, 61, 61, 26, 61, 12, 1, 1, 1, 1, 1, 1, 1, 148, 148, 201, 201, 201, 201, 201, 160, 160, 160, 148, 112, 112, 61, 26, 26, 1, 148, 148, 148, 148] 201
rigid atoms, others: [39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 836
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051920 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051920
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051920/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051920
Building REAL300025051921
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051921'
/scratch/stefan/7786831/working/building/REAL300025051921 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051921

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051921/0 /scratch/stefan/7786831/working/building/REAL300025051921 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 816)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/816
`/scratch/stefan/7786831/working/3D/816' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2CCC[C@H]2CF)CC1)

`REAL300025051921.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051921.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051921/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051921 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2CCC[C@H]2CF)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 7, 5, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 12, 25, 34, 68, 68, 68, 68, 68, 5, 1, 1, 1, 3, 3, 3, 19, 19, 19, 19, 19, 19, 19, 46, 1, 1, 25, 25, 68, 12, 5, 5, 3, 19, 19, 19, 19, 19, 19, 46, 46, 1, 1, 1, 1] 138
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 319
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: REAL300025051921 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2CCC[C@H]2CF)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 7, 5, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [38, 21, 12, 1, 1, 1, 1, 1, 1, 1, 38, 38, 62, 68, 68, 68, 68, 138, 138, 138, 138, 138, 138, 138, 138, 68, 68, 21, 21, 1, 38, 62, 62, 68, 138, 138, 138, 138, 138, 138, 138, 138, 68, 68, 68, 68] 138
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45])
total number of confs: 497
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051921 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2CCC[C@H]2CF)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 7, 5, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [57, 57, 57, 84, 97, 138, 138, 138, 138, 138, 24, 19, 10, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 19, 19, 84, 84, 138, 57, 24, 24, 10, 1, 1, 1, 1, 1, 1, 9, 9, 19, 19, 19, 19] 138
rigid atoms, others: [34, 35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45])
total number of confs: 445
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051921 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051921
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051921/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051921
Building REAL300025051922
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051922'
/scratch/stefan/7786831/working/building/REAL300025051922 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051922

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051922/0 /scratch/stefan/7786831/working/building/REAL300025051922 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 817)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/817
`/scratch/stefan/7786831/working/3D/817' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NOC(C3CCC3)=C2)CC1)

`REAL300025051922.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051922.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051922/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051922 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NOC(C3CCC3)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 5, 5, 5, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 35, 38, 77, 77, 77, 77, 77, 4, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 74, 74, 74, 15, 1, 1, 35, 35, 77, 16, 4, 4, 3, 74, 74, 74, 74, 74, 74, 74, 15, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051922 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NOC(C3CCC3)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 5, 5, 5, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [40, 24, 13, 1, 1, 1, 1, 1, 1, 1, 40, 40, 63, 77, 77, 77, 77, 96, 96, 96, 96, 201, 201, 201, 96, 77, 77, 24, 24, 1, 40, 63, 63, 77, 201, 201, 201, 201, 201, 201, 201, 96, 77, 77, 77, 77] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45])
total number of confs: 654
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051922 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NOC(C3CCC3)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 5, 5, 5, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [163, 163, 163, 186, 187, 201, 201, 201, 201, 201, 91, 74, 59, 59, 12, 59, 12, 12, 12, 1, 1, 1, 1, 1, 12, 74, 74, 186, 186, 201, 163, 91, 91, 59, 1, 1, 1, 1, 1, 1, 1, 12, 74, 74, 74, 74] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45])
total number of confs: 685
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051922 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NOC(C3CCC3)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 5, 5, 5, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 56, 56, 76, 78, 96, 96, 96, 96, 96, 19, 15, 11, 10, 1, 10, 1, 1, 1, 1, 1, 12, 12, 12, 1, 15, 15, 76, 76, 96, 56, 19, 19, 11, 12, 12, 12, 12, 12, 12, 12, 1, 15, 15, 15, 15] 201
rigid atoms, others: [41, 14, 16, 17, 18, 19, 20, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 336
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051922 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051922
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051922/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051922
Building REAL300025051923
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051923'
/scratch/stefan/7786831/working/building/REAL300025051923 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051923

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051923/0 /scratch/stefan/7786831/working/building/REAL300025051923 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 818)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/818
`/scratch/stefan/7786831/working/3D/818' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)[C@@H](O)[C@@H](C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051923.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051923.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051923/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051923 none CC(C)[C@@H](O)[C@@H](C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 200, 201, 201, 151, 200, 200, 151, 151, 151, 142, 75, 75, 29, 75, 13, 1, 1, 1, 1, 1, 1, 1, 151, 151, 201, 201, 201, 201, 201, 201, 201, 603, 200, 200, 200, 151, 142, 142, 75, 29, 29, 1, 151, 151, 151, 151] 603
rigid atoms, others: [44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48])
total number of confs: 1455
number of broken/clashed sets: 120
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051923 none CC(C)[C@@H](O)[C@@H](C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [13, 11, 13, 8, 11, 11, 2, 8, 8, 2, 2, 1, 1, 1, 6, 11, 11, 11, 39, 66, 151, 151, 151, 151, 151, 1, 1, 13, 13, 13, 13, 13, 13, 13, 33, 8, 8, 8, 2, 6, 6, 11, 39, 39, 151, 1, 1, 1, 1] 603
rigid atoms, others: [11, 12, 13, 46, 45, 48, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 410
number of broken/clashed sets: 120
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051923 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051923
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051923/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051923
Building REAL300025051924
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051924'
/scratch/stefan/7786831/working/building/REAL300025051924 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051924

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051924/0 /scratch/stefan/7786831/working/building/REAL300025051924 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 819)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/819
`/scratch/stefan/7786831/working/3D/819' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3C=CC=CC3=NO2)CC1)

`REAL300025051924.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051924.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051924/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051924 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3C=CC=CC3=NO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 30, 105, 119, 200, 200, 200, 200, 200, 6, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 105, 105, 200, 30, 6, 6, 3, 8, 8, 8, 8, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 555
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051924 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3C=CC=CC3=NO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 132, 200, 200, 200, 200, 201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 32, 32, 1, 65, 132, 132, 200, 201, 201, 201, 201, 200, 200, 200, 200] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 718
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051924 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3C=CC=CC3=NO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [50, 50, 50, 139, 149, 201, 201, 201, 201, 201, 13, 8, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 139, 139, 201, 50, 13, 13, 5, 1, 1, 1, 1, 8, 8, 8, 8] 201
rigid atoms, others: [34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 651
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051924 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051924
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051924/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051924
Building REAL300025051925
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051925'
/scratch/stefan/7786831/working/building/REAL300025051925 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051925

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051925/0 /scratch/stefan/7786831/working/building/REAL300025051925 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 820)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/820
`/scratch/stefan/7786831/working/3D/820' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC12CCC(C(=O)NC3(CNC(=O)CSC4=NNC(=O)[N-]4)CC3)(CC1)CO2)

`REAL300025051925.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051925.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051925/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051925 none CC12CCC(C(=O)NC3(CNC(=O)CSC4=NNC(=O)[N-]4)CC3)(CC1)CO2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 20, 20, 20, 66, 77, 117, 117, 117, 117, 117, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 20, 66, 66, 117, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5] 201
rigid atoms, others: [7, 8, 9, 42, 43, 44, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 45, 46, 47, 48, 49, 50])
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: REAL300025051925 none CC12CCC(C(=O)NC3(CNC(=O)CSC4=NNC(=O)[N-]4)CC3)(CC1)CO2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 4, 4, 5, 5, 11, 54, 54, 54, 139, 154, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 5, 11, 11, 54, 139, 139, 201, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 45, 46, 47, 48, 49, 50, 23, 24, 25, 26, 5, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 630
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051925 none CC12CCC(C(=O)NC3(CNC(=O)CSC4=NNC(=O)[N-]4)CC3)(CC1)CO2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 117, 117, 117, 117, 106, 62, 62, 27, 62, 12, 1, 1, 1, 1, 1, 1, 1, 117, 117, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 117, 106, 106, 62, 27, 27, 1, 117, 117, 117, 117, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [40, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 572
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051925 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051925
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051925/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051925
Building REAL300025051926
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051926'
/scratch/stefan/7786831/working/building/REAL300025051926 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051926

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051926/0 /scratch/stefan/7786831/working/building/REAL300025051926 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 821)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/821
`/scratch/stefan/7786831/working/3D/821' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=NC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(=O)N1)

`REAL300025051926.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051926.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051926/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051926 none CCC1=NC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 7, 21, 21, 21, 56, 60, 108, 109, 109, 109, 109, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 7, 7, 21, 56, 56, 109, 1, 1, 1, 1, 2] 201
rigid atoms, others: [8, 9, 10, 43, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 44])
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: REAL300025051926 none CCC1=NC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 7, 21, 21, 21, 56, 60, 108, 109, 109, 109, 109, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 1, 2, 7, 7, 21, 56, 56, 109, 2, 2, 2, 2, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 44, 24, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 320
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051926 none CCC1=NC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 109, 109, 109, 109, 109, 109, 109, 109, 73, 36, 36, 24, 36, 12, 1, 1, 1, 1, 1, 1, 1, 109, 109, 109, 109, 109, 201, 201, 201, 201, 201, 109, 109, 73, 73, 36, 24, 24, 1, 109, 109, 109, 109, 109] 201
rigid atoms, others: [39, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44])
total number of confs: 955
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051926 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051926
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051926/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051926
Building REAL300025051927
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051927'
/scratch/stefan/7786831/working/building/REAL300025051927 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051927

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051927/0 /scratch/stefan/7786831/working/building/REAL300025051927 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 822)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/822
`/scratch/stefan/7786831/working/3D/822' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=CN1CCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051927.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051927.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051927/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051927 none O=CN1CCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
137  conformations in input
total number of sets (complete confs): 137
using faster count positions algorithm for large data
unique positions, atoms: [13, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 7, 20, 20, 20, 57, 78, 118, 118, 118, 118, 118, 1, 1, 13, 9, 9, 9, 9, 9, 9, 9, 2, 7, 7, 20, 57, 57, 118, 1, 1, 1, 1] 137
rigid atoms, others: [43, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 352
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051927 none O=CN1CCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
137  conformations in input
total number of sets (complete confs): 137
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 24, 54, 54, 54, 94, 113, 137, 137, 137, 137, 137, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 9, 24, 24, 54, 94, 94, 137, 9, 9, 9, 9] 137
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 26, 27, 28, 29, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 447
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051927 none O=CN1CCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 118, 118, 118, 118, 93, 59, 59, 27, 59, 13, 1, 1, 1, 1, 1, 1, 1, 118, 118, 137, 137, 137, 137, 137, 137, 137, 137, 118, 93, 93, 59, 27, 27, 1, 118, 118, 118, 118] 137
rigid atoms, others: [39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 514
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051927 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051927
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051927/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051927
Building REAL300025051928
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051928'
/scratch/stefan/7786831/working/building/REAL300025051928 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051928

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051928/0 /scratch/stefan/7786831/working/building/REAL300025051928 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 823)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/823
`/scratch/stefan/7786831/working/3D/823' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1)

`REAL300025051928.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051928.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051928/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051928 none CC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 7, 30, 30, 30, 98, 115, 201, 201, 201, 201, 201, 1, 1, 3, 3, 3, 3, 3, 2, 7, 7, 30, 98, 98, 201, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 555
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051928 none CC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 10, 36, 36, 36, 103, 119, 201, 201, 201, 201, 201, 3, 3, 1, 2, 2, 2, 1, 3, 10, 10, 36, 103, 103, 201, 3, 3, 3, 3] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 23, 27] set([6, 7, 8, 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, 37, 38])
total number of confs: 572
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051928 none CC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 132, 59, 59, 29, 59, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 132, 132, 59, 29, 29, 1, 201, 201, 201, 201] 201
rigid atoms, others: [34, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 749
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051928 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051928/1 /scratch/stefan/7786831/working/building/REAL300025051928 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 824)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/824
`/scratch/stefan/7786831/working/3D/824' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N1)

`REAL300025051928.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051928.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051928/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051928 none CC1=NN=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', '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, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
160  conformations in input
total number of sets (complete confs): 160
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 7, 32, 32, 32, 79, 99, 160, 160, 160, 160, 160, 1, 1, 3, 3, 3, 3, 2, 7, 7, 32, 79, 79, 160, 1, 1, 1, 1, 3] 160
rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38])
total number of confs: 438
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051928 none CC1=NN=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', '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, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
160  conformations in input
total number of sets (complete confs): 160
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 10, 39, 39, 39, 90, 112, 160, 160, 160, 160, 160, 3, 3, 1, 2, 2, 2, 3, 10, 10, 39, 90, 90, 160, 3, 3, 3, 3, 1] 160
rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 23] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 476
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051928 none CC1=NN=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', '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, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
160  conformations in input
total number of sets (complete confs): 160
using faster count positions algorithm for large data
unique positions, atoms: [160, 160, 160, 160, 160, 160, 160, 160, 129, 68, 68, 31, 68, 13, 1, 1, 1, 1, 1, 1, 1, 160, 160, 160, 160, 160, 160, 160, 129, 129, 68, 31, 31, 1, 160, 160, 160, 160, 160] 160
rigid atoms, others: [33, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 593
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051928 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051928
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051928/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051928/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051928
Building REAL300025051929
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051929'
/scratch/stefan/7786831/working/building/REAL300025051929 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300025051929

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051929/0 /scratch/stefan/7786831/working/building/REAL300025051929 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 825)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/825
`/scratch/stefan/7786831/working/3D/825' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)[N@@H+]1CCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051929.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051929.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051929/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051929 none CC(C)(C)[N@@H+]1CCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
6  conformations in input
total number of sets (complete confs): 6
using default count positions algorithm for smaller data
unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 5, 5, 6, 6, 6, 6, 6, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 6, 1, 1, 1, 1] 6
rigid atoms, others: [11, 12, 13, 48, 49, 50, 51, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 25
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051929 none CC(C)(C)[N@@H+]1CCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 5, 5, 6, 2, 2, 2, 2] 6
rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 39, 40, 36, 38, 37] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 25
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051929 none CC(C)(C)[N@@H+]1CCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 6, 6, 4, 6, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 1, 6, 6, 6, 6] 6
rigid atoms, others: [47, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51])
total number of confs: 13
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051929 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051929/1 /scratch/stefan/7786831/working/building/REAL300025051929 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 826)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/826
`/scratch/stefan/7786831/working/3D/826' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)[N@H+]1CCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051929.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051929.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051929/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051929 none CC(C)(C)[N@H+]1CCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 8, 8, 14, 14, 14, 14, 14, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 8, 8, 14, 1, 1, 1, 1] 14
rigid atoms, others: [11, 12, 13, 48, 49, 50, 51, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 42
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: REAL300025051929 none CC(C)(C)[N@H+]1CCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 4, 4, 4, 8, 8, 14, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 4, 4, 4, 8, 8, 14, 2, 2, 2, 2] 14
rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 39, 40, 36, 38, 37] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 45
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051929 none CC(C)(C)[N@H+]1CCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 14, 14, 11, 14, 7, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 11, 11, 1, 14, 14, 14, 14] 14
rigid atoms, others: [47, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51])
total number of confs: 39
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051929 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `2'
/scratch/stefan/7786831/working/building/REAL300025051929/2 /scratch/stefan/7786831/working/building/REAL300025051929 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 2 (index: 827)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/827
`/scratch/stefan/7786831/working/3D/827' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)N1CCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051929.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300025051929.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051929/2/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`2.mol2' -> `2.mol2.original'
`output.mol2' -> `2.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051929 none CC(C)(C)N1CCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 29, 29, 29, 80, 92, 176, 176, 176, 176, 176, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 29, 80, 80, 176, 1, 1, 1, 1] 201
rigid atoms, others: [10, 11, 12, 47, 48, 49, 50, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 464
number of broken/clashed sets: 201
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051929 none CC(C)(C)N1CCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 4, 4, 4, 4, 17, 49, 49, 49, 112, 124, 201, 201, 201, 201, 201, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 4, 17, 17, 49, 112, 112, 201, 4, 4, 4, 4] 201
rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 39, 36, 38, 37] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 589
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051929 none CC(C)(C)N1CCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 176, 176, 176, 176, 139, 54, 54, 27, 54, 13, 1, 1, 1, 1, 1, 1, 1, 176, 176, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 176, 139, 139, 54, 27, 27, 1, 176, 176, 176, 176] 201
rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50])
total number of confs: 769
number of broken/clashed sets: 201
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051929 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051929
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
2: /scratch/stefan/7786831/working/building/REAL300025051929/2.*
1: /scratch/stefan/7786831/working/building/REAL300025051929/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051929/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051929
Building REAL300025051930
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051930'
/scratch/stefan/7786831/working/building/REAL300025051930 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051930

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051930/0 /scratch/stefan/7786831/working/building/REAL300025051930 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 828)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/828
`/scratch/stefan/7786831/working/3D/828' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1CC1(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051930.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051930.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051930/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051930 none O=C(CCC1CC1(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 5, 5, 5, 5, 15, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 10, 15, 27, 27, 27, 27, 1, 1, 1, 4, 7, 7, 7, 21, 32, 90, 90, 90, 90, 90, 1, 1, 10, 10, 17, 17, 27, 27, 27, 2, 4, 4, 7, 21, 21, 90, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 291
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051930 none O=C(CCC1CC1(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 5, 5, 5, 5, 15, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 9, 5, 1, 1, 1, 1, 1, 1, 27, 27, 27, 36, 55, 55, 55, 108, 139, 201, 201, 201, 201, 201, 27, 27, 9, 9, 5, 5, 1, 1, 1, 27, 36, 36, 55, 108, 108, 201, 27, 27, 27, 27] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 650
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051930 none O=C(CCC1CC1(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 5, 5, 5, 5, 5, 15, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [90, 90, 90, 176, 183, 201, 201, 201, 201, 90, 78, 50, 50, 25, 50, 12, 1, 1, 1, 1, 1, 1, 1, 90, 90, 176, 176, 191, 191, 201, 201, 201, 90, 78, 78, 50, 25, 25, 1, 90, 90, 90, 90] 201
rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 871
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051930 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051930
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051930/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051930
Building REAL300025051931
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051931'
/scratch/stefan/7786831/working/building/REAL300025051931 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051931

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051931/0 /scratch/stefan/7786831/working/building/REAL300025051931 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 829)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/829
`/scratch/stefan/7786831/working/3D/829' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCC(=O)C1CC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051931.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051931.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051931/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051931 none O=C(CCCC(=O)C1CC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 1, 11, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 8, 8, 10, 22, 22, 51, 51, 1, 1, 1, 3, 3, 3, 3, 9, 14, 48, 48, 48, 48, 48, 1, 1, 8, 8, 9, 9, 9, 10, 51, 51, 51, 51, 51, 2, 3, 3, 3, 9, 9, 48, 1, 1, 1, 1] 201
rigid atoms, others: [44, 10, 11, 12, 45, 46, 47, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
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: REAL300025051931 none O=C(CCCC(=O)C1CC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 1, 11, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [51, 42, 31, 28, 8, 1, 8, 1, 1, 1, 51, 51, 51, 63, 63, 63, 63, 115, 139, 201, 201, 201, 201, 201, 51, 51, 42, 42, 31, 31, 28, 28, 1, 1, 1, 1, 1, 51, 63, 63, 63, 115, 115, 201, 51, 51, 51, 51] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 706
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051931 none O=C(CCCC(=O)C1CC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 1, 11, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 48, 117, 122, 147, 194, 194, 201, 201, 48, 40, 40, 40, 24, 40, 12, 1, 1, 1, 1, 1, 1, 1, 48, 48, 117, 117, 136, 136, 135, 147, 201, 201, 201, 201, 201, 48, 40, 40, 40, 24, 24, 1, 48, 48, 48, 48] 201
rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47])
total number of confs: 882
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051931 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051931
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051931/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051931
Building REAL300025051932
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051932'
/scratch/stefan/7786831/working/building/REAL300025051932 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051932

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051932/0 /scratch/stefan/7786831/working/building/REAL300025051932 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 830)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/830
`/scratch/stefan/7786831/working/3D/830' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=NN(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1)

`REAL300025051932.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051932.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051932/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051932 none NC1=NN(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 8, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 10, 8, 2, 2, 2, 1, 1, 1, 7, 20, 20, 20, 63, 83, 178, 178, 178, 178, 178, 1, 1, 11, 11, 11, 11, 10, 10, 8, 8, 2, 7, 7, 20, 63, 63, 178, 1, 1, 1, 1, 11, 11] 201
rigid atoms, others: [39, 8, 9, 10, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 43, 44])
total number of confs: 461
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051932 none NC1=NN(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 8, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 4, 6, 11, 11, 11, 11, 23, 45, 45, 45, 103, 122, 201, 201, 201, 201, 201, 11, 11, 1, 1, 2, 2, 4, 4, 6, 6, 11, 23, 23, 45, 103, 103, 201, 11, 11, 11, 11, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 43, 44, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 603
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051932 none NC1=NN(CCC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 8, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 178, 178, 178, 178, 139, 67, 67, 27, 67, 12, 1, 1, 1, 1, 1, 1, 1, 178, 178, 201, 201, 201, 201, 201, 201, 201, 201, 178, 139, 139, 67, 27, 27, 1, 178, 178, 178, 178, 201, 201] 201
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42, 43, 44])
total number of confs: 786
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051932 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051932
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051932/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051932
Building REAL300025051933
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051933'
/scratch/stefan/7786831/working/building/REAL300025051933 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051933

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051933/0 /scratch/stefan/7786831/working/building/REAL300025051933 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 831)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/831
`/scratch/stefan/7786831/working/3D/831' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1)

`REAL300025051933.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051933.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051933/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051933 none CC1=NN=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 18, 18, 10, 2, 2, 2, 1, 1, 1, 6, 13, 13, 13, 41, 57, 136, 136, 136, 136, 136, 1, 1, 18, 18, 18, 18, 10, 10, 2, 6, 6, 13, 41, 41, 136, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 40, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
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: REAL300025051933 none CC1=NN=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 18, 33, 51, 51, 51, 105, 131, 201, 201, 201, 201, 201, 18, 18, 1, 2, 2, 2, 7, 7, 18, 33, 33, 51, 105, 105, 201, 18, 18, 18, 18] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 632
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051933 none CC1=NN=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 136, 136, 136, 136, 113, 70, 70, 27, 70, 13, 1, 1, 1, 1, 1, 1, 1, 136, 136, 201, 201, 201, 201, 201, 201, 136, 113, 113, 70, 27, 27, 1, 136, 136, 136, 136] 201
rigid atoms, others: [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, 34, 35, 37, 38, 39, 40])
total number of confs: 821
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051933 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051933
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051933/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051933
Building REAL300025051934
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051934'
/scratch/stefan/7786831/working/building/REAL300025051934 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051934

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051934/0 /scratch/stefan/7786831/working/building/REAL300025051934 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 832)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/832
`/scratch/stefan/7786831/working/3D/832' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CN=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051934.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051934.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051934/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051934 none CC1=CN=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 7, 29, 29, 29, 83, 106, 201, 201, 201, 201, 201, 1, 1, 3, 3, 3, 3, 3, 2, 7, 7, 29, 83, 83, 201, 1, 1, 1, 1, 3] 201
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40])
total number of confs: 518
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051934 none CC1=CN=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 13, 43, 43, 43, 108, 130, 201, 201, 201, 201, 201, 3, 3, 1, 2, 2, 2, 1, 3, 13, 13, 43, 108, 108, 201, 3, 3, 3, 3, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 40, 24, 28] set([7, 8, 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])
total number of confs: 592
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051934 none CC1=CN=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 139, 64, 64, 28, 64, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 139, 139, 64, 28, 28, 1, 201, 201, 201, 201, 201] 201
rigid atoms, others: [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, 33, 34, 36, 37, 38, 39, 40])
total number of confs: 745
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051934 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051934
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051934/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051934
Building REAL300025051935
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051935'
/scratch/stefan/7786831/working/building/REAL300025051935 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051935

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051935/0 /scratch/stefan/7786831/working/building/REAL300025051935 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 833)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/833
`/scratch/stefan/7786831/working/3D/833' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)C1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1)

`REAL300025051935.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051935.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051935/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051935 none CC(=O)C1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 4, 7, 4, 4, 2, 2, 2, 1, 1, 1, 7, 29, 29, 29, 89, 105, 198, 198, 198, 198, 198, 1, 1, 4, 4, 7, 7, 7, 4, 2, 7, 7, 29, 89, 89, 198, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 40, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
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: REAL300025051935 none CC(=O)C1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 4, 4, 4, 4, 12, 37, 37, 37, 98, 114, 200, 200, 200, 200, 200, 4, 4, 1, 1, 5, 5, 5, 1, 4, 12, 12, 37, 98, 98, 200, 4, 4, 4, 4] 201
rigid atoms, others: [1, 3, 4, 5, 6, 24, 25, 29] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 561
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051935 none CC(=O)C1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 200, 198, 198, 198, 198, 124, 50, 50, 29, 50, 13, 1, 1, 1, 1, 1, 1, 1, 198, 198, 200, 200, 201, 201, 201, 200, 198, 124, 124, 50, 29, 29, 1, 198, 198, 198, 198] 201
rigid atoms, others: [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, 34, 35, 37, 38, 39, 40])
total number of confs: 751
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051935 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051935
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051935/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051935
Building REAL300025051936
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051936'
/scratch/stefan/7786831/working/building/REAL300025051936 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051936

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051936/0 /scratch/stefan/7786831/working/building/REAL300025051936 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 834)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/834
`/scratch/stefan/7786831/working/3D/834' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)N1C=CC=C1)

`REAL300025051936.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051936.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051936/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051936 none CC(C)C(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)N1C=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 158, 158, 158, 158, 110, 55, 55, 25, 55, 13, 1, 1, 1, 1, 1, 1, 1, 158, 158, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 158, 110, 110, 55, 25, 25, 1, 158, 158, 158, 158, 201, 201, 201, 201] 201
rigid atoms, others: [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, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49])
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: REAL300025051936 none CC(C)C(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)N1C=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 2, 2, 2, 1, 1, 1, 7, 18, 18, 18, 60, 86, 158, 158, 158, 158, 158, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 7, 7, 18, 60, 60, 158, 1, 1, 1, 1, 8, 8, 8, 8] 201
rigid atoms, others: [6, 7, 8, 42, 43, 44, 45, 20, 21] set([0, 1, 2, 3, 4, 5, 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, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49])
total number of confs: 412
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051936 none CC(C)C(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)N1C=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 10, 10, 10, 10, 21, 36, 36, 36, 79, 121, 201, 201, 201, 201, 201, 10, 10, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 4, 10, 21, 21, 36, 79, 79, 201, 10, 10, 10, 10, 1, 1, 1, 1] 201
rigid atoms, others: [3, 46, 47, 48, 49, 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, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 574
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051936 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051936
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051936/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051936
Building REAL300025051937
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051937'
/scratch/stefan/7786831/working/building/REAL300025051937 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051937

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051937/0 /scratch/stefan/7786831/working/building/REAL300025051937 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 835)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/835
`/scratch/stefan/7786831/working/3D/835' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCC1(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1)

`REAL300025051937.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051937.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051937/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051937 none CSCC1(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [34, 18, 15, 8, 2, 2, 2, 1, 1, 1, 4, 6, 6, 6, 20, 32, 104, 104, 104, 104, 104, 1, 1, 15, 15, 34, 34, 34, 18, 18, 8, 8, 2, 4, 4, 6, 20, 20, 104, 1, 1, 1, 1, 15, 15, 15, 15] 201
rigid atoms, others: [39, 8, 9, 42, 7, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 43, 44, 45, 46])
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: REAL300025051937 none CSCC1(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 4, 1, 1, 1, 7, 15, 15, 15, 15, 25, 32, 32, 32, 77, 105, 198, 198, 198, 198, 198, 15, 15, 1, 1, 12, 12, 12, 4, 4, 7, 7, 15, 25, 25, 32, 77, 77, 198, 15, 15, 15, 15, 1, 1, 1, 1] 201
rigid atoms, others: [2, 3, 4, 43, 44, 45, 46, 23, 24] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 565
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051937 none CSCC1(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 198, 198, 169, 104, 104, 104, 104, 84, 69, 69, 30, 69, 13, 1, 1, 1, 1, 1, 1, 1, 104, 104, 198, 198, 201, 201, 201, 198, 198, 169, 169, 104, 84, 84, 69, 30, 30, 1, 104, 104, 104, 104, 198, 198, 198, 198] 201
rigid atoms, others: [38, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 836
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051937 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051937
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051937/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051937
Building REAL300025051938
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051938'
/scratch/stefan/7786831/working/building/REAL300025051938 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051938

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051938/0 /scratch/stefan/7786831/working/building/REAL300025051938 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 836)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/836
`/scratch/stefan/7786831/working/3D/836' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCCCC1)

`REAL300025051938.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051938.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051938/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051938 none N#CC1(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCCCC1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 14, 7, 2, 2, 2, 1, 1, 1, 7, 19, 19, 19, 62, 87, 180, 180, 180, 180, 180, 1, 1, 14, 14, 14, 14, 14, 7, 7, 2, 7, 7, 19, 62, 62, 180, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 201
rigid atoms, others: [36, 37, 6, 7, 8, 39, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
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: REAL300025051938 none N#CC1(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCCCC1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 14, 14, 14, 14, 25, 44, 44, 44, 93, 121, 201, 201, 201, 201, 201, 14, 14, 1, 1, 1, 1, 1, 8, 8, 14, 25, 25, 44, 93, 93, 201, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 22, 23, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 563
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051938 none N#CC1(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCCCC1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 198, 180, 180, 180, 180, 142, 66, 66, 30, 66, 13, 1, 1, 1, 1, 1, 1, 1, 180, 180, 201, 201, 201, 201, 201, 198, 198, 180, 142, 142, 66, 30, 30, 1, 180, 180, 180, 180, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 792
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051938 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051938
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051938/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051938
Building REAL300025051939
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051939'
/scratch/stefan/7786831/working/building/REAL300025051939 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051939

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051939/0 /scratch/stefan/7786831/working/building/REAL300025051939 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 837)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/837
`/scratch/stefan/7786831/working/3D/837' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@@H]2C(F)F)CC1)

`REAL300025051939.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051939.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051939/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051939 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@@H]2C(F)F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 38, 50, 154, 154, 154, 154, 154, 5, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 27, 27, 1, 1, 38, 38, 154, 13, 5, 5, 3, 14, 14, 27, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
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: REAL300025051939 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@@H]2C(F)F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [83, 34, 12, 1, 1, 1, 1, 1, 1, 1, 83, 83, 143, 154, 154, 154, 154, 198, 198, 198, 198, 198, 201, 201, 154, 154, 34, 34, 1, 83, 143, 143, 154, 198, 198, 201, 154, 154, 154, 154] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 781
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051939 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@@H]2C(F)F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 93, 110, 198, 198, 198, 198, 198, 21, 14, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 14, 14, 93, 93, 198, 45, 21, 21, 8, 1, 1, 7, 14, 14, 14, 14] 201
rigid atoms, others: [33, 34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39])
total number of confs: 564
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051939 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051939
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051939/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051939
Building REAL300025051940
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051940'
/scratch/stefan/7786831/working/building/REAL300025051940 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051940

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051940/0 /scratch/stefan/7786831/working/building/REAL300025051940 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 838)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/838
`/scratch/stefan/7786831/working/3D/838' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C(=O)NC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051940.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051940.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051940/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051940 none CCN1C(=O)NC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 11, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 8, 8, 8, 8, 8, 8, 2, 2, 2, 1, 1, 1, 7, 11, 11, 11, 36, 55, 122, 122, 122, 122, 122, 1, 1, 12, 12, 12, 12, 12, 8, 8, 2, 7, 7, 11, 36, 36, 122, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 10, 11, 12, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 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: REAL300025051940 none CCN1C(=O)NC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 11, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 8, 8, 18, 25, 25, 25, 53, 77, 145, 145, 145, 145, 145, 8, 8, 2, 2, 2, 2, 2, 1, 1, 8, 18, 18, 25, 53, 53, 145, 8, 8, 8, 8] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 372
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051940 none CCN1C(=O)NC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 11, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 145, 145, 145, 145, 145, 145, 122, 122, 122, 122, 97, 55, 55, 28, 55, 13, 1, 1, 1, 1, 1, 1, 1, 122, 122, 201, 201, 201, 201, 201, 145, 145, 122, 97, 97, 55, 28, 28, 1, 122, 122, 122, 122] 201
rigid atoms, others: [39, 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, 40, 41, 42, 43])
total number of confs: 863
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051940 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051940
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051940/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051940
Building REAL300025051941
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051941'
/scratch/stefan/7786831/working/building/REAL300025051941 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051941

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051941/0 /scratch/stefan/7786831/working/building/REAL300025051941 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 839)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/839
`/scratch/stefan/7786831/working/3D/839' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=COC(=O)N2)CC1)

`REAL300025051941.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051941.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051941/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051941 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=COC(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 12, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 60, 69, 120, 120, 120, 120, 120, 5, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 60, 60, 120, 22, 5, 5, 3, 13, 13, 1, 1, 1, 1] 146
rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32])
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: REAL300025051941 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=COC(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 12, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [63, 30, 13, 1, 1, 1, 1, 1, 1, 1, 63, 63, 98, 120, 120, 120, 120, 146, 146, 146, 146, 146, 120, 120, 30, 30, 1, 63, 98, 98, 120, 146, 146, 120, 120, 120, 120] 146
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 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])
total number of confs: 500
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051941 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=COC(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 12, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 120, 129, 146, 146, 146, 146, 146, 20, 13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 13, 120, 120, 146, 67, 20, 20, 7, 1, 1, 13, 13, 13, 13] 146
rigid atoms, others: [32, 14, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36])
total number of confs: 512
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051941 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051941/1 /scratch/stefan/7786831/working/building/REAL300025051941 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 840)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/840
`/scratch/stefan/7786831/working/3D/840' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=COC(=O)[N-]2)CC1)

`REAL300025051941.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051941.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051941/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051941 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=COC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 12, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 64, 113, 197, 197, 197, 197, 197, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 1, 1, 64, 64, 197, 23, 6, 6, 3, 7, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 480
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051941 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=COC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 12, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 40, 13, 1, 1, 1, 1, 1, 1, 1, 108, 108, 178, 197, 201, 201, 201, 201, 201, 201, 201, 201, 197, 197, 40, 40, 1, 108, 178, 178, 201, 201, 197, 197, 197, 197] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 770
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051941 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=COC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 12, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [35, 35, 35, 79, 127, 201, 201, 201, 201, 201, 13, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 7, 79, 79, 201, 35, 13, 13, 4, 1, 7, 7, 7, 7] 201
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 524
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051941 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051941
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051941/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051941/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051941
Building REAL300025051942
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051942'
/scratch/stefan/7786831/working/building/REAL300025051942 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051942

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051942/0 /scratch/stefan/7786831/working/building/REAL300025051942 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 841)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/841
`/scratch/stefan/7786831/working/3D/841' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC(O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051942.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051942.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051942/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051942 none CC=CC(O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 189, 177, 189, 177, 177, 177, 159, 85, 85, 33, 85, 13, 1, 1, 1, 1, 1, 1, 1, 177, 177, 201, 201, 201, 201, 201, 189, 567, 177, 159, 159, 85, 33, 33, 1, 177, 177, 177, 177] 603
rigid atoms, others: [36, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 1378
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051942 none CC=CC(O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 5, 2, 5, 2, 2, 1, 1, 1, 5, 9, 9, 9, 32, 59, 177, 177, 177, 177, 177, 1, 1, 17, 17, 17, 17, 17, 5, 15, 2, 5, 5, 9, 32, 32, 177, 1, 1, 1, 1] 603
rigid atoms, others: [37, 38, 7, 8, 9, 39, 40, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 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])
total number of confs: 390
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051942 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051942
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051942/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051942
Building REAL300025051943
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051943'
/scratch/stefan/7786831/working/building/REAL300025051943 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051943

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051943/0 /scratch/stefan/7786831/working/building/REAL300025051943 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 842)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/842
`/scratch/stefan/7786831/working/3D/842' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=CC=CNC3=N2)CC1)

`REAL300025051943.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051943.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051943/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051943 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=CC=CNC3=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 29, 106, 117, 200, 200, 200, 200, 200, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 106, 106, 200, 29, 6, 6, 3, 7, 7, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 551
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051943 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=CC=CNC3=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 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]
0  hydrogens 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, 31, 13, 1, 1, 1, 1, 1, 1, 1, 63, 63, 154, 200, 200, 200, 200, 201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 31, 31, 1, 63, 154, 154, 200, 201, 201, 201, 201, 201, 200, 200, 200, 200] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 758
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051943 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC3=CC=CNC3=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 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]
0  hydrogens 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, 131, 140, 201, 201, 201, 201, 201, 11, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 131, 131, 201, 45, 11, 11, 4, 1, 1, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42])
total number of confs: 616
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051943 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051943
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051943/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051943
Building REAL300025051944
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051944'
/scratch/stefan/7786831/working/building/REAL300025051944 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051944

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051944/0 /scratch/stefan/7786831/working/building/REAL300025051944 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 843)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/843
`/scratch/stefan/7786831/working/3D/843' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC[C@H](C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051944.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051944.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051944/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051944 none CCCC[C@H](C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 181, 99, 181, 181, 99, 99, 99, 91, 55, 55, 26, 55, 13, 1, 1, 1, 1, 1, 1, 1, 99, 99, 201, 201, 201, 201, 201, 201, 201, 201, 201, 181, 181, 181, 99, 91, 91, 55, 26, 26, 1, 99, 99, 99, 99] 201
rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47])
total number of confs: 878
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051944 none CCCC[C@H](C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 19, 19, 9, 2, 9, 9, 2, 2, 1, 1, 1, 4, 8, 8, 8, 23, 37, 99, 99, 99, 99, 99, 1, 1, 20, 20, 20, 20, 20, 19, 19, 19, 19, 9, 9, 9, 2, 4, 4, 8, 23, 23, 99, 1, 1, 1, 1] 201
rigid atoms, others: [9, 10, 11, 44, 45, 46, 47, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 292
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051944 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051944
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051944/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051944
Building REAL300025051945
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051945'
/scratch/stefan/7786831/working/building/REAL300025051945 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051945

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051945/0 /scratch/stefan/7786831/working/building/REAL300025051945 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 844)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/844
`/scratch/stefan/7786831/working/3D/844' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1F)

`REAL300025051945.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051945.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051945/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051945 none CNC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 15, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 14, 14, 14, 47, 62, 115, 115, 115, 115, 115, 1, 1, 5, 5, 5, 9, 9, 9, 9, 5, 5, 2, 4, 4, 14, 47, 47, 115, 1, 1, 1, 1, 5] 201
rigid atoms, others: [8, 9, 10, 43, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 44])
total number of confs: 304
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051945 none CNC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 15, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 41, 41, 41, 114, 137, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 2, 2, 2, 2, 1, 1, 5, 13, 13, 41, 114, 114, 201, 5, 5, 5, 5, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 44, 24, 25, 26, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 593
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051945 none CNC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 15, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 115, 115, 115, 115, 95, 62, 62, 29, 62, 13, 1, 1, 1, 1, 1, 1, 1, 115, 115, 201, 201, 201, 201, 201, 201, 201, 201, 201, 115, 95, 95, 62, 29, 29, 1, 115, 115, 115, 115, 201] 201
rigid atoms, others: [39, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44])
total number of confs: 573
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051945 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051945
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051945/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051945
Building REAL300025051946
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051946'
/scratch/stefan/7786831/working/building/REAL300025051946 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025051946

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051946/0 /scratch/stefan/7786831/working/building/REAL300025051946 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 845)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/845
`/scratch/stefan/7786831/working/3D/845' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)[NH+](C)C)

`REAL300025051946.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051946.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051946/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051946 none C[C@@H](C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)[NH+](C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', '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, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [31, 27, 31, 27, 27, 27, 26, 23, 23, 19, 23, 12, 1, 1, 1, 1, 1, 1, 1, 27, 27, 31, 31, 31, 31, 31, 31, 31, 27, 26, 26, 23, 19, 19, 1, 27, 27, 27, 27, 31, 31, 31, 31, 31, 31] 31
rigid atoms, others: [34, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 109
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: REAL300025051946 none C[C@@H](C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)[NH+](C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', '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, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 2, 5, 2, 2, 1, 1, 1, 4, 7, 7, 7, 14, 16, 27, 27, 27, 27, 27, 1, 1, 5, 10, 10, 10, 5, 5, 5, 2, 4, 4, 7, 14, 14, 27, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10] 31
rigid atoms, others: [35, 36, 5, 6, 7, 19, 20, 38, 37] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44])
total number of confs: 118
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051946 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051946/1 /scratch/stefan/7786831/working/building/REAL300025051946 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 846)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/846
`/scratch/stefan/7786831/working/3D/846' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)N(C)C)

`REAL300025051946.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051946.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051946/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051946 none C[C@@H](C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.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, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 10, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
158  conformations in input
total number of sets (complete confs): 158
using faster count positions algorithm for large data
unique positions, atoms: [158, 150, 158, 150, 150, 150, 140, 78, 78, 29, 78, 13, 1, 1, 1, 1, 1, 1, 1, 150, 150, 158, 158, 158, 158, 158, 158, 150, 140, 140, 78, 29, 29, 1, 150, 150, 150, 150, 158, 158, 158, 158, 158, 158] 158
rigid atoms, others: [33, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
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: REAL300025051946 none C[C@@H](C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.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, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 10, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
158  conformations in input
total number of sets (complete confs): 158
using faster count positions algorithm for large data
unique positions, atoms: [6, 2, 6, 2, 2, 1, 1, 1, 6, 23, 23, 23, 61, 98, 150, 150, 150, 150, 150, 1, 1, 6, 9, 9, 6, 6, 6, 2, 6, 6, 23, 61, 61, 150, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9] 158
rigid atoms, others: [34, 35, 36, 5, 6, 7, 19, 20, 37] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43])
total number of confs: 414
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051946 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051946
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025051946/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051946/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051946
Building REAL300025051947
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051947'
/scratch/stefan/7786831/working/building/REAL300025051947 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051947

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051947/0 /scratch/stefan/7786831/working/building/REAL300025051947 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 847)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/847
`/scratch/stefan/7786831/working/3D/847' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC=C(F)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051947.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051947.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051947/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051947 none CCC=C(F)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 15, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 136, 136, 134, 136, 134, 134, 134, 92, 41, 41, 25, 41, 13, 1, 1, 1, 1, 1, 1, 1, 134, 134, 201, 201, 201, 201, 201, 136, 134, 92, 92, 41, 25, 25, 1, 134, 134, 134, 134] 201
rigid atoms, others: [35, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39])
total number of confs: 901
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051947 none CCC=C(F)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 15, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 4, 4, 2, 4, 2, 2, 1, 1, 1, 7, 20, 20, 20, 53, 62, 134, 134, 134, 134, 134, 1, 1, 7, 7, 7, 7, 7, 4, 2, 7, 7, 20, 53, 53, 134, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 7, 8, 9, 39, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 366
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051947 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051947
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051947/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051947
Building REAL300025051948
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051948'
/scratch/stefan/7786831/working/building/REAL300025051948 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051948

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051948/0 /scratch/stefan/7786831/working/building/REAL300025051948 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 848)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/848
`/scratch/stefan/7786831/working/3D/848' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2C3(CC3)C23CC3)CC1)

`REAL300025051948.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051948.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051948/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051948 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2C3(CC3)C23CC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 16, 16, 57, 69, 157, 157, 157, 157, 157, 5, 1, 1, 1, 3, 3, 3, 20, 20, 20, 20, 20, 20, 1, 1, 57, 57, 157, 16, 5, 5, 3, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 42, 11, 12, 13, 44, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
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: REAL300025051948 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2C3(CC3)C23CC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [74, 29, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 135, 157, 157, 157, 157, 201, 201, 201, 201, 201, 201, 157, 157, 29, 29, 1, 74, 135, 135, 157, 201, 201, 201, 201, 201, 201, 201, 201, 201, 157, 157, 157, 157] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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: 737
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051948 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2C3(CC3)C23CC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [72, 72, 72, 124, 139, 201, 201, 201, 201, 201, 28, 20, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 20, 20, 124, 124, 201, 72, 28, 28, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44])
total number of confs: 623
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051948 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051948
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051948/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051948
Building REAL300025051949
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051949'
/scratch/stefan/7786831/working/building/REAL300025051949 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051949

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051949/0 /scratch/stefan/7786831/working/building/REAL300025051949 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 849)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/849
`/scratch/stefan/7786831/working/3D/849' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051949.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051949.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051949/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051949 none CCC=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 164, 164, 118, 118, 118, 118, 104, 56, 56, 27, 56, 13, 1, 1, 1, 1, 1, 1, 1, 118, 118, 201, 201, 201, 201, 201, 164, 164, 118, 104, 104, 56, 27, 27, 1, 118, 118, 118, 118] 201
rigid atoms, others: [35, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39])
total number of confs: 887
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051949 none CCC=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 9, 9, 2, 2, 2, 1, 1, 1, 4, 8, 8, 8, 25, 38, 118, 118, 118, 118, 118, 1, 1, 16, 16, 16, 16, 16, 9, 9, 2, 4, 4, 8, 25, 25, 118, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 6, 7, 8, 39, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 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: 286
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051949 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051949
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051949/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051949
Building REAL300025051950
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051950'
/scratch/stefan/7786831/working/building/REAL300025051950 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051950

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051950/0 /scratch/stefan/7786831/working/building/REAL300025051950 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 850)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/850
`/scratch/stefan/7786831/working/3D/850' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1N)

`REAL300025051950.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051950.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051950/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051950 none CN1N=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1N NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 2, 2, 2, 1, 1, 1, 7, 30, 30, 30, 90, 109, 201, 201, 201, 201, 201, 1, 1, 3, 3, 3, 3, 3, 2, 7, 7, 30, 90, 90, 201, 1, 1, 1, 1, 3, 3] 201
rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40])
total number of confs: 532
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051950 none CN1N=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1N NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 3, 3, 12, 43, 43, 43, 110, 130, 201, 201, 201, 201, 201, 3, 3, 1, 1, 2, 2, 2, 3, 12, 12, 43, 110, 110, 201, 3, 3, 3, 3, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 23, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 596
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051950 none CN1N=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1N NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 142, 68, 68, 29, 68, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 142, 142, 68, 29, 29, 1, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [34, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40])
total number of confs: 751
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051950 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051950
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051950/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051950
Building REAL300025051951
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051951'
/scratch/stefan/7786831/working/building/REAL300025051951 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051951

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051951/0 /scratch/stefan/7786831/working/building/REAL300025051951 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 851)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/851
`/scratch/stefan/7786831/working/3D/851' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(F)(F)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051951.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051951.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051951/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051951 none CCC(F)(F)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 15, 15, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 194, 201, 201, 140, 140, 140, 140, 117, 70, 70, 29, 70, 13, 1, 1, 1, 1, 1, 1, 1, 140, 140, 201, 201, 201, 201, 201, 194, 194, 140, 117, 117, 70, 29, 29, 1, 140, 140, 140, 140] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41])
total number of confs: 882
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051951 none CCC(F)(F)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 15, 15, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 14, 7, 14, 14, 2, 2, 2, 1, 1, 1, 4, 8, 8, 8, 31, 49, 140, 140, 140, 140, 140, 1, 1, 15, 15, 15, 15, 15, 7, 7, 2, 4, 4, 8, 31, 31, 140, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 8, 9, 10, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
total number of confs: 329
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051951 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051951
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051951/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051951
Building REAL300025051952
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051952'
/scratch/stefan/7786831/working/building/REAL300025051952 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051952

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051952/0 /scratch/stefan/7786831/working/building/REAL300025051952 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 852)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/852
`/scratch/stefan/7786831/working/3D/852' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NOC=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051952.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051952.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051952/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051952 none CC1=NOC=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 12, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 24, 24, 9, 2, 2, 2, 1, 1, 1, 5, 8, 8, 8, 21, 31, 90, 90, 90, 90, 90, 1, 1, 24, 24, 24, 24, 9, 9, 2, 5, 5, 8, 21, 21, 90, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 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: REAL300025051952 none CC1=NOC=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 12, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 24, 24, 24, 24, 32, 51, 51, 51, 98, 129, 201, 201, 201, 201, 201, 24, 24, 2, 2, 2, 1, 6, 6, 24, 32, 32, 51, 98, 98, 201, 24, 24, 24, 24] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 616
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051952 none CC1=NOC=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 12, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 165, 90, 90, 90, 90, 79, 49, 49, 27, 49, 13, 1, 1, 1, 1, 1, 1, 1, 90, 90, 201, 201, 201, 201, 165, 165, 90, 79, 79, 49, 27, 27, 1, 90, 90, 90, 90] 201
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41])
total number of confs: 773
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051952 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051952
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051952/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051952
Building REAL300025051953
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051953'
/scratch/stefan/7786831/working/building/REAL300025051953 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051953

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051953/0 /scratch/stefan/7786831/working/building/REAL300025051953 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 853)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/853
`/scratch/stefan/7786831/working/3D/853' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CSN=N2)CC1)

`REAL300025051953.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051953.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051953/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051953 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CSN=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 14, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 17, 45, 58, 154, 154, 154, 154, 154, 5, 1, 1, 1, 3, 3, 3, 18, 26, 26, 26, 26, 1, 1, 45, 45, 154, 17, 5, 5, 3, 18, 18, 26, 1, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 390
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051953 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CSN=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 14, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [77, 35, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 133, 154, 154, 154, 154, 196, 201, 201, 201, 201, 154, 154, 35, 35, 1, 77, 133, 133, 154, 196, 196, 201, 154, 154, 154, 154] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 827
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051953 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CSN=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 14, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [65, 65, 65, 120, 129, 201, 201, 201, 201, 201, 33, 26, 22, 22, 4, 22, 1, 1, 1, 1, 1, 1, 26, 26, 120, 120, 201, 65, 33, 33, 22, 4, 4, 1, 26, 26, 26, 26] 201
rigid atoms, others: [33, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 616
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051953 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051953
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051953/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051953
Building REAL300025051954
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051954'
/scratch/stefan/7786831/working/building/REAL300025051954 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051954

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051954/0 /scratch/stefan/7786831/working/building/REAL300025051954 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 854)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/854
`/scratch/stefan/7786831/working/3D/854' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=CC1=CC=CN=C1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051954.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051954.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051954/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051954 none CC(=CC1=CC=CN=C1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 2, 11, 11, 18, 18, 18, 18, 18, 2, 2, 1, 1, 1, 4, 9, 9, 9, 25, 37, 79, 79, 79, 79, 79, 1, 1, 11, 11, 11, 11, 18, 18, 18, 18, 2, 4, 4, 9, 25, 25, 79, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 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: REAL300025051954 none CC(=CC1=CC=CN=C1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 18, 18, 18, 18, 38, 55, 55, 55, 98, 124, 201, 201, 201, 201, 201, 18, 18, 3, 3, 3, 3, 1, 1, 1, 1, 18, 38, 38, 55, 98, 98, 201, 18, 18, 18, 18] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 608
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051954 none CC(=CC1=CC=CN=C1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [165, 79, 165, 165, 201, 201, 201, 201, 201, 79, 79, 79, 72, 46, 46, 27, 46, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 165, 165, 165, 165, 201, 201, 201, 201, 79, 72, 72, 46, 27, 27, 1, 79, 79, 79, 79] 201
rigid atoms, others: [41, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 627
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051954 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051954
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051954/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051954
Building REAL300025051955
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051955'
/scratch/stefan/7786831/working/building/REAL300025051955 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051955

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051955/0 /scratch/stefan/7786831/working/building/REAL300025051955 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 855)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/855
`/scratch/stefan/7786831/working/3D/855' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCCC1)

`REAL300025051955.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051955.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051955/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051955 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 2, 2, 2, 1, 1, 1, 7, 24, 24, 24, 70, 77, 157, 158, 158, 158, 158, 1, 1, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 24, 70, 70, 158, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3] 201
rigid atoms, others: [35, 36, 5, 6, 7, 19, 20, 38, 37] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025051955 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 3, 11, 42, 42, 42, 110, 118, 200, 201, 201, 201, 201, 3, 3, 1, 1, 1, 1, 2, 2, 2, 3, 11, 11, 42, 110, 110, 201, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 44, 45, 46, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 577
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051955 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 158, 158, 158, 158, 111, 48, 48, 28, 48, 13, 1, 1, 1, 1, 1, 1, 1, 158, 158, 201, 201, 201, 201, 201, 201, 201, 158, 111, 111, 48, 28, 28, 1, 158, 158, 158, 158, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [34, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 692
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051955 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051955
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051955/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051955
Building REAL300025051956
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051956'
/scratch/stefan/7786831/working/building/REAL300025051956 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051956

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051956/0 /scratch/stefan/7786831/working/building/REAL300025051956 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 856)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/856
`/scratch/stefan/7786831/working/3D/856' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1)

`REAL300025051956.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051956.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051956/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051956 none COCC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 8, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 6, 11, 11, 11, 27, 38, 125, 125, 125, 125, 125, 1, 1, 2, 20, 20, 20, 8, 8, 2, 2, 6, 6, 11, 27, 27, 125, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 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: REAL300025051956 none COCC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 8, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 11, 11, 11, 27, 38, 125, 125, 125, 125, 125, 2, 2, 1, 20, 20, 20, 8, 8, 1, 2, 6, 6, 11, 27, 27, 125, 2, 2, 2, 2] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 25, 31] set([0, 1, 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])
total number of confs: 281
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051956 none COCC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 125, 125, 125, 125, 125, 125, 125, 125, 89, 51, 51, 26, 51, 12, 1, 1, 1, 1, 1, 1, 1, 125, 125, 125, 201, 201, 201, 201, 201, 125, 125, 89, 89, 51, 26, 26, 1, 125, 125, 125, 125] 201
rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 896
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051956 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051956
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051956/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051956
Building REAL300025051957
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051957'
/scratch/stefan/7786831/working/building/REAL300025051957 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051957

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051957/0 /scratch/stefan/7786831/working/building/REAL300025051957 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 857)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/857
`/scratch/stefan/7786831/working/3D/857' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C[C@H]2COC(=O)N2)CC1)

`REAL300025051957.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051957.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051957/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051957 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C[C@H]2COC(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 32, 39, 82, 82, 82, 82, 82, 5, 1, 1, 1, 3, 3, 3, 21, 48, 48, 48, 48, 48, 48, 1, 1, 32, 32, 82, 13, 5, 5, 3, 21, 21, 48, 48, 48, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051957 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C[C@H]2COC(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [49, 25, 12, 1, 1, 1, 1, 1, 1, 1, 49, 49, 73, 82, 82, 82, 82, 187, 201, 201, 201, 201, 201, 201, 82, 82, 25, 25, 1, 49, 73, 73, 82, 187, 187, 201, 201, 201, 82, 82, 82, 82] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 848
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051957 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C[C@H]2COC(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [113, 113, 113, 155, 167, 201, 201, 201, 201, 201, 60, 48, 32, 32, 6, 32, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 155, 155, 201, 113, 60, 60, 32, 6, 6, 1, 1, 1, 48, 48, 48, 48] 201
rigid atoms, others: [35, 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, 38, 39, 40, 41])
total number of confs: 676
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051957 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051957
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051957/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051957
Building REAL300025051958
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051958'
/scratch/stefan/7786831/working/building/REAL300025051958 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051958

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051958/0 /scratch/stefan/7786831/working/building/REAL300025051958 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 858)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/858
`/scratch/stefan/7786831/working/3D/858' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025051958.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051958.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051958/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051958 none CC(C)C1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 8, 15, 8, 8, 2, 2, 2, 1, 1, 1, 4, 9, 9, 9, 26, 42, 114, 114, 114, 114, 114, 1, 1, 8, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 2, 4, 4, 9, 26, 26, 114, 1, 1, 1, 1, 8, 8] 201
rigid atoms, others: [8, 9, 10, 43, 44, 45, 46, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 47, 48])
total number of confs: 294
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051958 none CC(C)C1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 8, 8, 8, 22, 43, 43, 43, 96, 138, 201, 201, 201, 201, 201, 8, 8, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 8, 22, 22, 43, 96, 96, 201, 8, 8, 8, 8, 1, 1] 201
rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 47, 48, 35, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 605
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051958 none CC(C)C1CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 114, 114, 114, 114, 93, 60, 60, 27, 60, 13, 1, 1, 1, 1, 1, 1, 1, 114, 114, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 114, 93, 93, 60, 27, 27, 1, 114, 114, 114, 114, 201, 201] 201
rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48])
total number of confs: 726
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051958 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051958
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051958/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051958
Building REAL300025051959
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051959'
/scratch/stefan/7786831/working/building/REAL300025051959 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051959

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051959/0 /scratch/stefan/7786831/working/building/REAL300025051959 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 859)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/859
`/scratch/stefan/7786831/working/3D/859' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CN=C1C#N)

`REAL300025051959.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051959.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051959/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051959 none CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CN=C1C#N NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.1', 'N.1', '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, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 21, 21, 21, 68, 82, 144, 144, 144, 144, 144, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 21, 68, 68, 144, 1, 1, 1, 1, 5] 201
rigid atoms, others: [6, 38, 7, 8, 41, 39, 40, 20, 21] set([0, 1, 2, 3, 4, 5, 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, 36, 37, 42])
total number of confs: 377
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051959 none CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CN=C1C#N NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.1', 'N.1', '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, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 57, 57, 57, 131, 154, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2, 1, 5, 13, 13, 57, 131, 131, 201, 5, 5, 5, 5, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 42, 22, 23, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 632
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051959 none CC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CN=C1C#N NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.1', 'N.1', '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, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 144, 144, 144, 144, 123, 80, 80, 34, 80, 13, 1, 1, 1, 1, 1, 1, 1, 144, 144, 201, 201, 201, 201, 201, 201, 201, 201, 201, 144, 123, 123, 80, 34, 34, 1, 144, 144, 144, 144, 201] 201
rigid atoms, others: [37, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 624
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051959 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051959
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051959/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051959
Building REAL300025051960
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051960'
/scratch/stefan/7786831/working/building/REAL300025051960 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051960

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051960/0 /scratch/stefan/7786831/working/building/REAL300025051960 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 860)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/860
`/scratch/stefan/7786831/working/3D/860' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(C)(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)[NH+](C)C)

`REAL300025051960.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051960.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051960/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051960 none C=CCC(C)(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)[NH+](C)C NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [25, 25, 21, 21, 21, 21, 21, 21, 21, 19, 19, 14, 19, 11, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 25, 25, 25, 25, 25, 21, 21, 21, 21, 21, 21, 19, 14, 14, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 25
rigid atoms, others: [41, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 86
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: REAL300025051960 none C=CCC(C)(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)[NH+](C)C NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [7, 5, 3, 2, 3, 2, 2, 1, 1, 1, 3, 4, 4, 4, 7, 8, 21, 21, 21, 21, 21, 1, 1, 3, 3, 3, 3, 7, 7, 7, 5, 5, 3, 3, 3, 2, 3, 3, 4, 7, 7, 21, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3] 25
rigid atoms, others: [7, 8, 9, 42, 43, 44, 45, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 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, 41, 46, 47, 48, 49, 50, 51])
total number of confs: 74
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051960 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051960
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051960/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051960
Building REAL300025051961
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051961'
/scratch/stefan/7786831/working/building/REAL300025051961 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051961

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051961/0 /scratch/stefan/7786831/working/building/REAL300025051961 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 861)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/861
`/scratch/stefan/7786831/working/3D/861' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCOC1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051961.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051961.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051961/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051961 none CC1CCOC1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 6, 24, 24, 24, 65, 75, 195, 195, 195, 195, 195, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 6, 6, 24, 65, 65, 195, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 46, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
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: REAL300025051961 none CC1CCOC1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 17, 52, 52, 52, 119, 128, 201, 201, 201, 201, 201, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 5, 17, 17, 52, 119, 119, 201, 5, 5, 5, 5] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 33, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 619
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051961 none CC1CCOC1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 195, 195, 195, 195, 142, 57, 57, 30, 57, 13, 1, 1, 1, 1, 1, 1, 1, 195, 195, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 195, 142, 142, 57, 30, 30, 1, 195, 195, 195, 195] 201
rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46])
total number of confs: 764
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051961 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051961
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051961/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051961
Building REAL300025051962
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051962'
/scratch/stefan/7786831/working/building/REAL300025051962 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051962

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051962/0 /scratch/stefan/7786831/working/building/REAL300025051962 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 862)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/862
`/scratch/stefan/7786831/working/3D/862' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C(Cl)CCOC2)CC1)

`REAL300025051962.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051962.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051962/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051962 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C(Cl)CCOC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 16, 5, 5, 12, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 26, 89, 103, 185, 185, 185, 185, 185, 6, 1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 12, 1, 1, 89, 89, 185, 26, 6, 6, 3, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 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: REAL300025051962 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C(Cl)CCOC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 16, 5, 5, 12, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 35, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 139, 185, 185, 185, 185, 201, 201, 201, 201, 201, 201, 185, 185, 35, 35, 1, 78, 139, 139, 185, 201, 201, 201, 201, 201, 201, 185, 185, 185, 185] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 710
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051962 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C(Cl)CCOC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 16, 5, 5, 12, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 143, 156, 201, 201, 201, 201, 201, 21, 12, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 12, 12, 143, 143, 201, 60, 21, 21, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41])
total number of confs: 665
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051962 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051962
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051962/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051962
Building REAL300025051963
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051963'
/scratch/stefan/7786831/working/building/REAL300025051963 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051963

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051963/0 /scratch/stefan/7786831/working/building/REAL300025051963 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 863)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/863
`/scratch/stefan/7786831/working/3D/863' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1)

`REAL300025051963.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051963.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051963/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051963 none NC1=CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 7, 7, 5, 2, 2, 2, 1, 1, 1, 6, 22, 22, 22, 62, 74, 150, 150, 150, 150, 150, 1, 1, 7, 7, 7, 7, 7, 7, 5, 5, 2, 6, 6, 22, 62, 62, 150, 1, 1, 1, 1, 7, 7] 201
rigid atoms, others: [39, 8, 9, 10, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 43, 44])
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: REAL300025051963 none NC1=CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 8, 8, 8, 8, 20, 37, 37, 37, 90, 121, 201, 201, 201, 201, 201, 8, 8, 1, 1, 2, 2, 1, 1, 5, 5, 8, 20, 20, 37, 90, 90, 201, 8, 8, 8, 8, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 44, 24, 25, 28, 29] set([6, 7, 8, 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, 42])
total number of confs: 558
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051963 none NC1=CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 150, 150, 150, 150, 110, 50, 50, 26, 50, 13, 1, 1, 1, 1, 1, 1, 1, 150, 150, 201, 201, 201, 201, 201, 201, 201, 201, 150, 110, 110, 50, 26, 26, 1, 150, 150, 150, 150, 201, 201] 201
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42, 43, 44])
total number of confs: 826
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051963 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051963
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051963/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051963
Building REAL300025051964
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051964'
/scratch/stefan/7786831/working/building/REAL300025051964 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051964

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051964/0 /scratch/stefan/7786831/working/building/REAL300025051964 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 864)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/864
`/scratch/stefan/7786831/working/3D/864' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CNC(=O)C2)CC1)

`REAL300025051964.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051964.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051964/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051964 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CNC(=O)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 73, 89, 156, 156, 156, 156, 156, 5, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 1, 1, 73, 73, 156, 22, 5, 5, 3, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 429
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051964 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CNC(=O)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [70, 32, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 128, 156, 156, 156, 156, 201, 201, 201, 201, 201, 156, 156, 32, 32, 1, 70, 128, 128, 156, 201, 201, 201, 201, 201, 201, 156, 156, 156, 156] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 736
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051964 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CNC(=O)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [73, 73, 73, 147, 161, 201, 201, 201, 201, 201, 24, 15, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 15, 15, 147, 147, 201, 73, 24, 24, 9, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15] 201
rigid atoms, others: [32, 33, 34, 35, 36, 14, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40])
total number of confs: 670
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051964 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051964
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051964/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051964
Building REAL300025051965
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051965'
/scratch/stefan/7786831/working/building/REAL300025051965 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051965

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051965/0 /scratch/stefan/7786831/working/building/REAL300025051965 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 865)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/865
`/scratch/stefan/7786831/working/3D/865' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCCC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025051965.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051965.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051965/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051965 none CC1CCCC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 22, 22, 10, 2, 2, 2, 1, 1, 1, 4, 7, 7, 7, 21, 30, 96, 96, 96, 96, 96, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10, 10, 2, 4, 4, 7, 21, 21, 96, 1, 1, 1, 1, 22, 22] 201
rigid atoms, others: [9, 10, 11, 46, 47, 48, 49, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51])
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: REAL300025051965 none CC1CCCC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 22, 22, 22, 22, 47, 65, 65, 65, 102, 125, 201, 201, 201, 201, 201, 22, 22, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 22, 47, 47, 65, 102, 102, 201, 22, 22, 22, 22, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 36, 34, 50, 35, 51, 25, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 651
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051965 none CC1CCCC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 189, 96, 96, 96, 96, 86, 51, 51, 23, 51, 13, 1, 1, 1, 1, 1, 1, 1, 96, 96, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 189, 189, 96, 86, 86, 51, 23, 23, 1, 96, 96, 96, 96, 201, 201] 201
rigid atoms, others: [45, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51])
total number of confs: 837
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051965 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051965
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051965/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051965
Building REAL300025051966
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051966'
/scratch/stefan/7786831/working/building/REAL300025051966 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051966

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051966/0 /scratch/stefan/7786831/working/building/REAL300025051966 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 866)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/866
`/scratch/stefan/7786831/working/3D/866' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(=O)OC1(C)C)

`REAL300025051966.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051966.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051966/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051966 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(=O)OC1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', '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, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 5, 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, 7, 2, 2, 2, 1, 1, 1, 7, 27, 27, 27, 72, 89, 194, 194, 194, 194, 194, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 7, 7, 27, 72, 72, 194, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7] 201
rigid atoms, others: [37, 6, 7, 40, 39, 19, 20, 38, 5] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46])
total number of confs: 476
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051966 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(=O)OC1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', '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, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 6, 6, 7, 7, 21, 50, 50, 50, 107, 129, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 21, 21, 50, 107, 107, 201, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 21, 22, 23, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 607
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051966 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(=O)OC1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', '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, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 194, 194, 194, 194, 139, 74, 74, 30, 74, 13, 1, 1, 1, 1, 1, 1, 1, 194, 194, 201, 201, 201, 201, 201, 201, 201, 201, 201, 194, 139, 139, 74, 30, 30, 1, 194, 194, 194, 194, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [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, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 726
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051966 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051966
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051966/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051966
Building REAL300025051967
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051967'
/scratch/stefan/7786831/working/building/REAL300025051967 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051967

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051967/0 /scratch/stefan/7786831/working/building/REAL300025051967 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 867)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/867
`/scratch/stefan/7786831/working/3D/867' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCSC(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051967.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051967.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051967/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051967 none CCCCSC(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 14, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 148, 115, 91, 115, 91, 91, 91, 76, 59, 59, 38, 59, 12, 1, 1, 1, 1, 1, 1, 1, 91, 91, 201, 201, 201, 201, 201, 201, 201, 201, 201, 115, 115, 115, 115, 91, 76, 76, 59, 38, 38, 1, 91, 91, 91, 91] 201
rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48])
total number of confs: 835
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051967 none CCCCSC(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 14, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 28, 28, 12, 6, 2, 6, 2, 2, 1, 1, 1, 3, 5, 5, 5, 23, 36, 91, 91, 91, 91, 91, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 6, 2, 3, 3, 5, 23, 23, 91, 1, 1, 1, 1] 201
rigid atoms, others: [9, 10, 11, 45, 46, 47, 48, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 282
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051967 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051967
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051967/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051967
Building REAL300025051968
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051968'
/scratch/stefan/7786831/working/building/REAL300025051968 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051968

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051968/0 /scratch/stefan/7786831/working/building/REAL300025051968 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 868)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/868
`/scratch/stefan/7786831/working/3D/868' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1N)

`REAL300025051968.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051968.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051968/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051968 none CC1=CC(C)=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1N NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', '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, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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: [6, 6, 6, 6, 6, 2, 2, 2, 1, 1, 1, 6, 22, 22, 22, 52, 59, 145, 145, 145, 145, 145, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 6, 6, 22, 52, 52, 145, 1, 1, 1, 1, 6, 6, 6] 201
rigid atoms, others: [43, 8, 9, 10, 23, 44, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 45, 46, 47])
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: REAL300025051968 none CC1=CC(C)=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1N NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', '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, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 20, 66, 66, 66, 127, 136, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 6, 20, 20, 66, 127, 127, 201, 6, 6, 6, 6, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 45, 46, 47, 24, 25, 26, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 644
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051968 none CC1=CC(C)=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1N NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', '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, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 145, 145, 145, 145, 101, 48, 48, 27, 48, 12, 1, 1, 1, 1, 1, 1, 1, 145, 145, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 145, 101, 101, 48, 27, 27, 1, 145, 145, 145, 145, 201, 201, 201] 201
rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 654
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051968 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051968
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051968/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051968
Building REAL300025051969
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051969'
/scratch/stefan/7786831/working/building/REAL300025051969 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051969

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051969/0 /scratch/stefan/7786831/working/building/REAL300025051969 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 869)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/869
`/scratch/stefan/7786831/working/3D/869' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)CC(C)(C)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051969.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051969.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051969/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051969 none CC(=O)CC(C)(C)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 182, 153, 182, 182, 129, 129, 129, 129, 117, 88, 88, 32, 88, 13, 1, 1, 1, 1, 1, 1, 1, 129, 129, 201, 201, 201, 201, 201, 182, 182, 182, 182, 182, 182, 153, 153, 129, 117, 117, 88, 32, 32, 1, 129, 129, 129, 129] 201
rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49])
total number of confs: 841
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051969 none CC(=O)CC(C)(C)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 20, 11, 4, 11, 11, 2, 2, 2, 1, 1, 1, 4, 9, 9, 9, 33, 56, 129, 129, 129, 129, 129, 1, 1, 20, 20, 20, 20, 20, 11, 11, 11, 11, 11, 11, 4, 4, 2, 4, 4, 9, 33, 33, 129, 1, 1, 1, 1] 201
rigid atoms, others: [10, 11, 12, 46, 47, 48, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 343
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051969 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051969
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051969/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051969
Building REAL300025051970
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051970'
/scratch/stefan/7786831/working/building/REAL300025051970 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051970

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051970/0 /scratch/stefan/7786831/working/building/REAL300025051970 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 870)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/870
`/scratch/stefan/7786831/working/3D/870' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3=CC=CC=C3N2)CC1)

`REAL300025051970.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051970.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051970/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051970 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3=CC=CC=C3N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 73, 80, 156, 156, 156, 156, 156, 6, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 73, 73, 156, 24, 6, 6, 3, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 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: REAL300025051970 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3=CC=CC=C3N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [60, 31, 13, 1, 1, 1, 1, 1, 1, 1, 60, 60, 132, 156, 156, 156, 156, 201, 201, 201, 201, 201, 201, 201, 201, 156, 156, 31, 31, 1, 60, 132, 132, 156, 201, 201, 201, 201, 201, 201, 201, 201, 156, 156, 156, 156] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45])
total number of confs: 760
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051970 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3=CC=CC=C3N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [53, 53, 53, 130, 137, 201, 201, 201, 201, 201, 16, 10, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 130, 130, 201, 53, 16, 16, 7, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44, 45])
total number of confs: 616
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051970 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051970
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051970/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051970
Building REAL300025051971
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051971'
/scratch/stefan/7786831/working/building/REAL300025051971 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051971

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051971/0 /scratch/stefan/7786831/working/building/REAL300025051971 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 871)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/871
`/scratch/stefan/7786831/working/3D/871' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=CN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=C1)

`REAL300025051971.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051971.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051971/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051971 none NC1=CN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 6, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 9, 2, 2, 2, 1, 1, 1, 6, 18, 18, 18, 57, 73, 160, 160, 160, 160, 160, 1, 1, 13, 13, 13, 13, 13, 9, 9, 2, 6, 6, 18, 57, 57, 160, 1, 1, 1, 1, 13] 201
rigid atoms, others: [37, 38, 7, 8, 9, 39, 40, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 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, 41])
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: REAL300025051971 none NC1=CN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 6, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 6, 13, 13, 13, 13, 28, 52, 52, 52, 109, 124, 201, 201, 201, 201, 201, 13, 13, 1, 1, 2, 2, 1, 6, 6, 13, 28, 28, 52, 109, 109, 201, 13, 13, 13, 13, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 41, 23, 24, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 626
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051971 none NC1=CN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 6, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 160, 160, 160, 160, 113, 56, 56, 29, 56, 13, 1, 1, 1, 1, 1, 1, 1, 160, 160, 201, 201, 201, 201, 201, 201, 201, 160, 113, 113, 56, 29, 29, 1, 160, 160, 160, 160, 201] 201
rigid atoms, others: [36, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41])
total number of confs: 825
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051971 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051971
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051971/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051971
Building REAL300025051972
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051972'
/scratch/stefan/7786831/working/building/REAL300025051972 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051972

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051972/0 /scratch/stefan/7786831/working/building/REAL300025051972 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 872)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/872
`/scratch/stefan/7786831/working/3D/872' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC=C(N)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025051972.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051972.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051972/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051972 none CCC1=CC=C(N)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 9, 9, 4, 9, 9, 9, 2, 2, 2, 1, 1, 1, 6, 9, 9, 9, 26, 38, 94, 94, 94, 94, 94, 1, 1, 9, 17, 17, 17, 17, 17, 9, 9, 9, 9, 2, 6, 6, 9, 26, 26, 94, 1, 1, 1, 1, 9] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47])
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: REAL300025051972 none CCC1=CC=C(N)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 22, 25, 25, 25, 47, 64, 120, 120, 120, 120, 120, 9, 9, 1, 3, 3, 3, 2, 2, 1, 1, 2, 2, 9, 22, 22, 25, 47, 47, 120, 9, 9, 9, 9, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 7, 47, 26] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 333
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051972 none CCC1=CC=C(N)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 120, 120, 117, 120, 120, 120, 94, 94, 94, 94, 75, 48, 48, 26, 48, 13, 1, 1, 1, 1, 1, 1, 1, 94, 94, 120, 201, 201, 201, 201, 201, 120, 120, 120, 120, 94, 75, 75, 48, 26, 26, 1, 94, 94, 94, 94, 120] 201
rigid atoms, others: [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, 40, 41, 43, 44, 45, 46, 47])
total number of confs: 901
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051972 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051972
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051972/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051972
Building REAL300025051973
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051973'
/scratch/stefan/7786831/working/building/REAL300025051973 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051973

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051973/0 /scratch/stefan/7786831/working/building/REAL300025051973 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 873)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/873
`/scratch/stefan/7786831/working/3D/873' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=NON=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051973.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051973.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051973/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051973 none NC1=NON=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 8, 12, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 6, 27, 27, 27, 117, 132, 201, 201, 201, 201, 201, 1, 1, 4, 4, 2, 6, 6, 27, 117, 117, 201, 1, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 568
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051973 none NC1=NON=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 8, 12, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 39, 39, 39, 125, 138, 201, 201, 201, 201, 201, 4, 4, 1, 1, 4, 11, 11, 39, 125, 125, 201, 4, 4, 4, 4] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 579
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051973 none NC1=NON=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 8, 12, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 173, 79, 79, 31, 79, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 173, 173, 79, 31, 31, 1, 201, 201, 201, 201] 201
rigid atoms, others: [32, 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, 33, 34, 35, 36])
total number of confs: 746
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051973 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051973
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051973/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051973
Building REAL300025051974
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051974'
/scratch/stefan/7786831/working/building/REAL300025051974 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051974

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051974/0 /scratch/stefan/7786831/working/building/REAL300025051974 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 874)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/874
`/scratch/stefan/7786831/working/3D/874' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN(CCO)N=N2)CC1)

`REAL300025051974.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051974.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051974/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051974 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN(CCO)N=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 12, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [16, 16, 16, 40, 44, 101, 101, 101, 101, 101, 4, 1, 1, 1, 3, 3, 3, 17, 17, 17, 60, 68, 17, 17, 1, 1, 40, 40, 101, 16, 4, 4, 3, 17, 60, 60, 68, 68, 204, 1, 1, 1, 1] 603
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 688
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051974 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN(CCO)N=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 12, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [49, 26, 13, 1, 1, 1, 1, 1, 1, 1, 49, 49, 85, 101, 101, 101, 101, 148, 148, 148, 201, 201, 148, 148, 101, 101, 26, 26, 1, 49, 85, 85, 101, 148, 201, 201, 201, 201, 603, 101, 101, 101, 101] 603
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 1376
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051974 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN(CCO)N=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 12, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [61, 61, 61, 105, 106, 148, 148, 148, 148, 148, 21, 17, 13, 13, 1, 13, 1, 1, 1, 1, 9, 15, 1, 1, 17, 17, 105, 105, 148, 61, 21, 21, 13, 1, 9, 9, 15, 15, 45, 17, 17, 17, 17] 603
rigid atoms, others: [33, 14, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 575
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051974 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051974
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051974/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051974
Building REAL300025051975
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051975'
/scratch/stefan/7786831/working/building/REAL300025051975 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051975

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051975/0 /scratch/stefan/7786831/working/building/REAL300025051975 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 875)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/875
`/scratch/stefan/7786831/working/3D/875' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(COC(F)(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051975.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051975.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051975/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051975 none O=C(COC(F)(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 5, 15, 15, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [64, 64, 64, 156, 201, 201, 201, 201, 64, 59, 44, 44, 22, 44, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 156, 156, 64, 59, 59, 44, 22, 22, 1, 64, 64, 64, 64] 201
rigid atoms, others: [32, 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, 33, 34, 35, 36])
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: REAL300025051975 none O=C(COC(F)(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 5, 15, 15, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 13, 38, 58, 59, 59, 1, 1, 1, 4, 13, 13, 13, 27, 29, 64, 64, 64, 64, 64, 1, 1, 13, 13, 2, 4, 4, 13, 27, 27, 64, 1, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 336
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051975 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051975
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051975/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051975
Building REAL300025051976
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051976'
/scratch/stefan/7786831/working/building/REAL300025051976 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051976

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051976/0 /scratch/stefan/7786831/working/building/REAL300025051976 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 876)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/876
`/scratch/stefan/7786831/working/3D/876' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2CNC(=O)N2)CC1)

`REAL300025051976.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051976.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051976/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051976 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2CNC(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [23, 23, 23, 71, 84, 142, 142, 142, 142, 142, 6, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 10, 1, 1, 71, 71, 142, 23, 6, 6, 3, 10, 10, 10, 10, 1, 1, 1, 1] 148
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 400
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051976 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2CNC(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [68, 34, 12, 1, 1, 1, 1, 1, 1, 1, 68, 68, 125, 142, 142, 142, 142, 148, 148, 148, 148, 148, 148, 142, 142, 34, 34, 1, 68, 125, 125, 142, 148, 148, 148, 148, 142, 142, 142, 142] 148
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 567
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051976 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2CNC(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [46, 46, 46, 101, 110, 148, 148, 148, 148, 148, 16, 10, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 10, 10, 101, 101, 148, 46, 16, 16, 7, 1, 1, 1, 1, 10, 10, 10, 10] 148
rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39])
total number of confs: 467
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051976 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051976
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051976/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051976
Building REAL300025051977
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051977'
/scratch/stefan/7786831/working/building/REAL300025051977 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051977

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051977/0 /scratch/stefan/7786831/working/building/REAL300025051977 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 877)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/877
`/scratch/stefan/7786831/working/3D/877' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=CS2)CC1)

`REAL300025051977.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051977.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051977/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051977 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=CS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 31, 31, 115, 132, 197, 197, 197, 197, 197, 6, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 1, 1, 115, 115, 197, 31, 6, 6, 3, 11, 11, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31])
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: REAL300025051977 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=CS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [81, 34, 13, 1, 1, 1, 1, 1, 1, 1, 81, 81, 154, 197, 197, 197, 197, 201, 201, 201, 201, 197, 197, 34, 34, 1, 81, 154, 154, 197, 201, 201, 197, 197, 197, 197] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 25] set([0, 1, 2, 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])
total number of confs: 738
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051977 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=CS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [50, 50, 50, 131, 145, 201, 201, 201, 201, 201, 18, 11, 7, 6, 1, 6, 1, 1, 1, 1, 1, 11, 11, 131, 131, 201, 50, 18, 18, 7, 1, 1, 11, 11, 11, 11] 201
rigid atoms, others: [14, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35])
total number of confs: 615
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051977 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051977
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051977/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051977
Building REAL300025051978
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051978'
/scratch/stefan/7786831/working/building/REAL300025051978 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051978

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051978/0 /scratch/stefan/7786831/working/building/REAL300025051978 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 878)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/878
`/scratch/stefan/7786831/working/3D/878' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=CC(F)=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1N)

`REAL300025051978.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051978.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051978/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051978 none NC1=CC(F)=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1N NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 6]
dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 7, 23, 23, 23, 49, 64, 135, 135, 135, 135, 135, 1, 1, 9, 9, 9, 9, 9, 9, 2, 7, 7, 23, 49, 49, 135, 1, 1, 1, 1, 9, 9] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: REAL300025051978 none NC1=CC(F)=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1N NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 6]
dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
201  conformations 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, 9, 9, 29, 63, 63, 63, 110, 127, 201, 201, 201, 201, 201, 9, 9, 1, 1, 2, 2, 1, 1, 9, 29, 29, 63, 110, 110, 201, 9, 9, 9, 9, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 25, 26, 29, 30] set([8, 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, 43])
total number of confs: 611
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051978 none NC1=CC(F)=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1N NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 6]
dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
201  conformations 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, 135, 135, 135, 96, 52, 52, 26, 52, 13, 1, 1, 1, 1, 1, 1, 1, 135, 135, 201, 201, 201, 201, 201, 201, 135, 96, 96, 52, 26, 26, 1, 135, 135, 135, 135, 201, 201] 201
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41, 42, 43])
total number of confs: 603
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051978 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051978
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051978/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051978
Building REAL300025051979
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051979'
/scratch/stefan/7786831/working/building/REAL300025051979 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051979

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051979/0 /scratch/stefan/7786831/working/building/REAL300025051979 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 879)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/879
`/scratch/stefan/7786831/working/3D/879' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(CCO)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051979.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051979.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051979/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051979 none CC1=NN(CCO)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 5, 12, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 4, 15, 19, 4, 2, 2, 2, 1, 1, 1, 4, 8, 8, 8, 25, 44, 133, 133, 133, 133, 133, 1, 1, 4, 4, 4, 15, 15, 19, 19, 57, 4, 2, 4, 4, 8, 25, 25, 133, 1, 1, 1, 1] 603
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
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: REAL300025051979 none CC1=NN(CCO)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 5, 12, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 6, 8, 1, 1, 1, 4, 4, 4, 4, 10, 19, 19, 19, 54, 77, 173, 173, 173, 173, 173, 4, 4, 2, 2, 2, 6, 6, 8, 8, 24, 1, 4, 10, 10, 19, 54, 54, 173, 4, 4, 4, 4] 603
rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 35] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 477
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051979 none CC1=NN(CCO)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 5, 12, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [173, 173, 173, 173, 173, 201, 201, 173, 133, 133, 133, 133, 111, 59, 59, 28, 59, 13, 1, 1, 1, 1, 1, 1, 1, 133, 133, 173, 173, 173, 201, 201, 201, 201, 603, 173, 133, 111, 111, 59, 28, 28, 1, 133, 133, 133, 133] 603
rigid atoms, others: [42, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46])
total number of confs: 1365
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051979 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051979
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051979/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051979
Building REAL300025051980
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051980'
/scratch/stefan/7786831/working/building/REAL300025051980 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051980

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051980/0 /scratch/stefan/7786831/working/building/REAL300025051980 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 880)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/880
`/scratch/stefan/7786831/working/3D/880' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC[NH+]1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051980.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051980.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051980/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051980 none O=C(CC[NH+]1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [2, 2, 2, 6, 9, 9, 9, 9, 9, 9, 1, 1, 1, 5, 8, 8, 8, 15, 22, 39, 39, 39, 39, 39, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 5, 5, 8, 15, 15, 39, 1, 1, 1, 1] 45
rigid atoms, others: [10, 11, 12, 45, 46, 47, 48, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
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: REAL300025051980 none O=C(CC[NH+]1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [9, 3, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 10, 14, 14, 14, 19, 27, 45, 45, 45, 45, 45, 9, 9, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 10, 10, 14, 19, 19, 45, 9, 9, 9, 9] 45
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 35, 36, 37, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 115
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051980 none O=C(CC[NH+]1CCCC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [39, 39, 39, 45, 45, 45, 45, 45, 45, 45, 39, 39, 38, 38, 26, 38, 12, 1, 1, 1, 1, 1, 1, 1, 39, 39, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 39, 39, 39, 38, 26, 26, 1, 39, 39, 39, 39] 45
rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48])
total number of confs: 157
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051980 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051980
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051980/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051980
Building REAL300025051981
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051981'
/scratch/stefan/7786831/working/building/REAL300025051981 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051981

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051981/0 /scratch/stefan/7786831/working/building/REAL300025051981 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 881)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/881
`/scratch/stefan/7786831/working/3D/881' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(NC(C)=O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051981.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051981.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051981/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051981 none CCCC(NC(C)=O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 1, 5, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 158, 135, 158, 161, 161, 161, 135, 135, 135, 111, 66, 66, 33, 66, 13, 1, 1, 1, 1, 1, 1, 1, 135, 135, 201, 201, 201, 201, 201, 201, 201, 158, 161, 161, 161, 161, 135, 111, 111, 66, 33, 33, 1, 135, 135, 135, 135] 201
rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48])
total number of confs: 928
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051981 none CCCC(NC(C)=O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 1, 5, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 13, 5, 2, 5, 8, 8, 8, 2, 2, 1, 1, 1, 5, 10, 10, 10, 34, 49, 135, 135, 135, 135, 135, 1, 1, 16, 16, 16, 16, 16, 13, 13, 5, 8, 8, 8, 8, 2, 5, 5, 10, 34, 34, 135, 1, 1, 1, 1] 201
rigid atoms, others: [10, 11, 12, 45, 46, 47, 48, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 360
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051981 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051981
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051981/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051981
Building REAL300025051982
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051982'
/scratch/stefan/7786831/working/building/REAL300025051982 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051982

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051982/0 /scratch/stefan/7786831/working/building/REAL300025051982 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 882)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/882
`/scratch/stefan/7786831/working/3D/882' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=C1C#N)

`REAL300025051982.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051982.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051982/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051982 none CC1=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=C1C#N NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 32, 32, 32, 95, 113, 198, 199, 199, 199, 199, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 32, 95, 95, 199, 1, 1, 1, 1, 4, 4] 201
rigid atoms, others: [37, 6, 7, 8, 39, 40, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 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, 36, 41, 42])
total number of confs: 542
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051982 none CC1=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=C1C#N NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 4, 4, 4, 4, 14, 42, 42, 42, 108, 121, 200, 201, 201, 201, 201, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 4, 14, 14, 42, 108, 108, 201, 4, 4, 4, 4, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 41, 42, 22, 23, 24, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 585
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051982 none CC1=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=C1C#N NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 199, 199, 199, 140, 59, 59, 29, 59, 13, 1, 1, 1, 1, 1, 1, 1, 199, 199, 201, 201, 201, 201, 201, 201, 201, 201, 199, 140, 140, 59, 29, 29, 1, 199, 199, 199, 199, 201, 201] 201
rigid atoms, others: [36, 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, 37, 38, 39, 40, 41, 42])
total number of confs: 735
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051982 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051982
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051982/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051982
Building REAL300025051983
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051983'
/scratch/stefan/7786831/working/building/REAL300025051983 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051983

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051983/0 /scratch/stefan/7786831/working/building/REAL300025051983 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 883)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/883
`/scratch/stefan/7786831/working/3D/883' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1N)

`REAL300025051983.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051983.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051983/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051983 none CC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1N NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 7, 26, 26, 26, 68, 80, 160, 160, 160, 160, 160, 1, 1, 7, 7, 7, 7, 7, 7, 2, 7, 7, 26, 68, 68, 160, 1, 1, 1, 1, 7, 7] 201
rigid atoms, others: [36, 37, 38, 7, 8, 9, 39, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41])
total number of confs: 410
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051983 none CC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1N NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
201  conformations 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, 7, 7, 16, 49, 49, 49, 111, 126, 201, 201, 201, 201, 201, 7, 7, 1, 1, 2, 2, 2, 1, 7, 16, 16, 49, 111, 111, 201, 7, 7, 7, 7, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 23, 24, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 589
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051983 none CC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1N NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 160, 160, 160, 160, 120, 63, 63, 30, 63, 13, 1, 1, 1, 1, 1, 1, 1, 160, 160, 201, 201, 201, 201, 201, 201, 160, 120, 120, 63, 30, 30, 1, 160, 160, 160, 160, 201, 201] 201
rigid atoms, others: [35, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41])
total number of confs: 656
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051983 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051983
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051983/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051983
Building REAL300025051984
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051984'
/scratch/stefan/7786831/working/building/REAL300025051984 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051984

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051984/0 /scratch/stefan/7786831/working/building/REAL300025051984 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 884)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/884
`/scratch/stefan/7786831/working/3D/884' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: [N-]=[N+]=NCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051984.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051984.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051984/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051984 none [N-]=[N+]=NCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.1', 'N.1', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 8, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 193, 176, 91, 91, 91, 91, 77, 52, 52, 26, 52, 12, 1, 1, 1, 1, 1, 1, 1, 91, 91, 193, 193, 176, 176, 91, 77, 77, 52, 26, 26, 1, 91, 91, 91, 91] 201
rigid atoms, others: [33, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 846
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051984 none [N-]=[N+]=NCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.1', 'N.1', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 8, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [49, 49, 15, 10, 2, 2, 2, 1, 1, 1, 3, 5, 5, 5, 17, 28, 91, 91, 91, 91, 91, 1, 1, 15, 15, 10, 10, 2, 3, 3, 5, 17, 17, 91, 1, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 280
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051984 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051984
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051984/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051984
Building REAL300025051985
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051985'
/scratch/stefan/7786831/working/building/REAL300025051985 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051985

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051985/0 /scratch/stefan/7786831/working/building/REAL300025051985 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 885)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/885
`/scratch/stefan/7786831/working/3D/885' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C=C(CO)N=N2)CC1)

`REAL300025051985.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051985.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051985/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051985 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C=C(CO)N=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 1, 1, 5, 12, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [16, 16, 16, 34, 35, 67, 67, 67, 67, 67, 4, 1, 1, 1, 3, 3, 3, 19, 40, 40, 40, 80, 40, 40, 1, 1, 34, 34, 67, 16, 4, 4, 3, 19, 19, 40, 80, 80, 240, 1, 1, 1, 1] 603
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 698
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051985 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C=C(CO)N=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 1, 1, 5, 12, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [34, 20, 13, 1, 1, 1, 1, 1, 1, 1, 34, 34, 62, 67, 67, 67, 67, 147, 201, 201, 201, 201, 201, 201, 67, 67, 20, 20, 1, 34, 62, 62, 67, 147, 147, 201, 201, 201, 603, 67, 67, 67, 67] 603
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 1274
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051985 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C=C(CO)N=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 1, 1, 5, 12, 8, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [119, 119, 119, 174, 174, 201, 201, 201, 201, 201, 52, 40, 32, 32, 7, 32, 1, 1, 1, 1, 1, 8, 1, 1, 40, 40, 174, 174, 201, 119, 52, 52, 32, 7, 7, 1, 8, 8, 24, 40, 40, 40, 40] 603
rigid atoms, others: [35, 16, 17, 18, 19, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 800
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051985 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051985
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051985/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051985
Building REAL300025051986
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051986'
/scratch/stefan/7786831/working/building/REAL300025051986 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051986

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051986/0 /scratch/stefan/7786831/working/building/REAL300025051986 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 886)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/886
`/scratch/stefan/7786831/working/3D/886' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCOCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051986.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051986.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051986/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051986 none C#CCOCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 176, 158, 89, 89, 89, 89, 76, 50, 50, 29, 50, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 201, 201, 201, 158, 158, 89, 76, 76, 50, 29, 29, 1, 89, 89, 89, 89] 201
rigid atoms, others: [34, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 870
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051986 none C#CCOCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [36, 36, 13, 6, 2, 2, 2, 1, 1, 1, 3, 5, 5, 5, 16, 28, 89, 89, 89, 89, 89, 1, 1, 36, 36, 36, 6, 6, 2, 3, 3, 5, 16, 16, 89, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 295
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051986 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051986
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051986/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051986
Building REAL300025051987
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051987'
/scratch/stefan/7786831/working/building/REAL300025051987 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051987

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051987/0 /scratch/stefan/7786831/working/building/REAL300025051987 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 887)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/887
`/scratch/stefan/7786831/working/3D/887' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=NN=CO2)CC1)

`REAL300025051987.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051987.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051987/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051987 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=NN=CO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 32, 42, 114, 114, 114, 114, 114, 4, 1, 1, 1, 3, 3, 3, 22, 41, 41, 41, 41, 1, 1, 32, 32, 114, 13, 4, 4, 3, 22, 22, 41, 1, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 336
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051987 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=NN=CO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 29, 13, 1, 1, 1, 1, 1, 1, 1, 60, 60, 95, 114, 114, 114, 114, 177, 201, 201, 201, 201, 114, 114, 29, 29, 1, 60, 95, 95, 114, 177, 177, 201, 114, 114, 114, 114] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 780
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051987 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=NN=CO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 144, 155, 201, 201, 201, 201, 201, 55, 41, 29, 29, 5, 29, 1, 1, 1, 1, 1, 1, 41, 41, 144, 144, 201, 88, 55, 55, 29, 5, 5, 1, 41, 41, 41, 41] 201
rigid atoms, others: [33, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 687
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051987 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051987
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051987/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051987
Building REAL300025051988
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051988'
/scratch/stefan/7786831/working/building/REAL300025051988 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051988

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051988/0 /scratch/stefan/7786831/working/building/REAL300025051988 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 888)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/888
`/scratch/stefan/7786831/working/3D/888' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)SCCO1)

`REAL300025051988.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051988.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051988/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051988 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)SCCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 5, 5, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 2, 2, 1, 1, 1, 6, 24, 24, 24, 68, 84, 171, 171, 171, 171, 171, 1, 1, 5, 5, 5, 5, 5, 5, 5, 2, 6, 6, 24, 68, 68, 171, 1, 1, 1, 1, 5, 5, 5, 5] 201
rigid atoms, others: [35, 36, 5, 6, 7, 19, 20, 38, 37] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42])
total number of confs: 424
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051988 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)SCCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 5, 5, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 5, 16, 54, 54, 54, 115, 134, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 1, 2, 2, 2, 5, 16, 16, 54, 115, 115, 201, 5, 5, 5, 5, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 601
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051988 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)SCCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 5, 5, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 171, 171, 171, 171, 118, 52, 52, 27, 52, 12, 1, 1, 1, 1, 1, 1, 1, 171, 171, 201, 201, 201, 201, 201, 201, 201, 171, 118, 118, 52, 27, 27, 1, 171, 171, 171, 171, 201, 201, 201, 201] 201
rigid atoms, others: [34, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 707
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051988 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051988
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051988/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051988
Building REAL300025051989
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051989'
/scratch/stefan/7786831/working/building/REAL300025051989 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300025051989

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051989/0 /scratch/stefan/7786831/working/building/REAL300025051989 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 889)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/889
`/scratch/stefan/7786831/working/3D/889' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(CCO)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051989.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051989.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051989/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051989 none CN(CCO)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
477  conformations in input
total number of sets (complete confs): 477
using faster count positions algorithm for large data
unique positions, atoms: [159, 159, 159, 159, 159, 149, 149, 149, 149, 126, 86, 86, 31, 86, 13, 1, 1, 1, 1, 1, 1, 1, 149, 149, 159, 159, 159, 159, 159, 159, 159, 477, 159, 159, 149, 126, 126, 86, 31, 31, 1, 149, 149, 149, 149] 477
rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 1084
number of broken/clashed sets: 105
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051989 none CN(CCO)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
477  conformations in input
total number of sets (complete confs): 477
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 6, 8, 2, 2, 2, 1, 1, 1, 6, 14, 14, 14, 55, 82, 149, 149, 149, 149, 149, 1, 1, 6, 6, 6, 6, 6, 8, 8, 24, 6, 6, 2, 6, 6, 14, 55, 55, 149, 1, 1, 1, 1] 477
rigid atoms, others: [43, 8, 9, 10, 23, 44, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
total number of confs: 418
number of broken/clashed sets: 105
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051989 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025051989/1 /scratch/stefan/7786831/working/building/REAL300025051989 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 890)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/890
`/scratch/stefan/7786831/working/3D/890' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@H+](CCO)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051989.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025051989.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051989/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051989 none C[N@H+](CCO)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [15, 15, 15, 15, 15, 15, 13, 13, 13, 13, 12, 12, 12, 10, 12, 8, 1, 1, 1, 1, 1, 1, 1, 13, 13, 15, 15, 15, 15, 15, 15, 15, 45, 15, 15, 13, 12, 12, 12, 10, 10, 1, 13, 13, 13, 13] 45
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 90
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: REAL300025051989 none C[N@H+](CCO)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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, 3, 5, 5, 6, 6, 2, 2, 2, 1, 1, 1, 3, 4, 4, 4, 6, 6, 13, 13, 13, 13, 13, 1, 1, 5, 5, 5, 6, 6, 6, 6, 18, 3, 3, 2, 3, 3, 4, 6, 6, 13, 1, 1, 1, 1] 45
rigid atoms, others: [43, 9, 10, 11, 44, 45, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 82
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051989 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `2'
/scratch/stefan/7786831/working/building/REAL300025051989/2 /scratch/stefan/7786831/working/building/REAL300025051989 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 2 (index: 891)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/891
`/scratch/stefan/7786831/working/3D/891' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@@H+](CCO)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051989.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300025051989.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051989/2/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: REAL300025051989 none C[N@@H+](CCO)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [15, 15, 15, 15, 15, 15, 13, 13, 13, 13, 12, 12, 12, 10, 12, 8, 1, 1, 1, 1, 1, 1, 1, 13, 13, 15, 15, 15, 15, 15, 15, 15, 45, 15, 15, 13, 12, 12, 12, 10, 10, 1, 13, 13, 13, 13] 45
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 90
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: REAL300025051989 none C[N@@H+](CCO)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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, 3, 5, 5, 6, 6, 2, 2, 2, 1, 1, 1, 3, 4, 4, 4, 6, 6, 13, 13, 13, 13, 13, 1, 1, 5, 5, 5, 6, 6, 6, 6, 18, 3, 3, 2, 3, 3, 4, 6, 6, 13, 1, 1, 1, 1] 45
rigid atoms, others: [43, 9, 10, 11, 44, 45, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 82
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051989 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051989
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
2: /scratch/stefan/7786831/working/building/REAL300025051989/2.*
1: /scratch/stefan/7786831/working/building/REAL300025051989/1.*
0: /scratch/stefan/7786831/working/building/REAL300025051989/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051989
Building REAL300025051990
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051990'
/scratch/stefan/7786831/working/building/REAL300025051990 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051990

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051990/0 /scratch/stefan/7786831/working/building/REAL300025051990 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 892)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/892
`/scratch/stefan/7786831/working/3D/892' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C(Cl)C=N2)CC1)

`REAL300025051990.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051990.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051990/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051990 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C(Cl)C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 16, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [32, 32, 32, 111, 118, 201, 201, 201, 201, 201, 7, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 1, 1, 111, 111, 201, 32, 7, 7, 3, 6, 6, 1, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33])
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: REAL300025051990 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C(Cl)C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 16, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [61, 30, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 145, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 30, 30, 1, 61, 145, 145, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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])
total number of confs: 742
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051990 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CN=C(Cl)C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 16, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [46, 46, 46, 129, 132, 201, 201, 201, 201, 201, 11, 6, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 129, 129, 201, 46, 11, 11, 4, 1, 1, 6, 6, 6, 6] 201
rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37])
total number of confs: 599
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051990 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051990
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051990/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051990
Building REAL300025051991
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051991'
/scratch/stefan/7786831/working/building/REAL300025051991 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051991

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051991/0 /scratch/stefan/7786831/working/building/REAL300025051991 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 893)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/893
`/scratch/stefan/7786831/working/3D/893' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCS2)CC1)

`REAL300025051991.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051991.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051991/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051991 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 21, 21, 64, 77, 169, 169, 169, 169, 169, 6, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 1, 1, 64, 64, 169, 21, 6, 6, 3, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 428
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051991 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [75, 33, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 139, 169, 169, 169, 169, 201, 201, 201, 201, 169, 169, 33, 33, 1, 75, 139, 139, 169, 201, 201, 201, 201, 201, 201, 201, 169, 169, 169, 169] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 25] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 765
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051991 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [64, 64, 64, 126, 136, 201, 201, 201, 201, 201, 23, 15, 9, 9, 1, 9, 1, 1, 1, 1, 1, 15, 15, 126, 126, 201, 64, 23, 23, 9, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15] 201
rigid atoms, others: [32, 33, 34, 35, 36, 14, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40])
total number of confs: 636
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051991 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051991
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051991/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051991
Building REAL300025051992
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051992'
/scratch/stefan/7786831/working/building/REAL300025051992 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051992

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051992/0 /scratch/stefan/7786831/working/building/REAL300025051992 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 894)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/894
`/scratch/stefan/7786831/working/3D/894' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(O)(CCC)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051992.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051992.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051992/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051992 none CCCC(O)(CCC)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [200, 200, 177, 166, 177, 171, 201, 201, 100, 100, 100, 100, 86, 60, 60, 26, 60, 13, 1, 1, 1, 1, 1, 1, 1, 100, 100, 200, 200, 200, 200, 200, 200, 200, 531, 201, 199, 201, 201, 201, 201, 201, 166, 166, 100, 86, 86, 60, 26, 26, 1, 100, 100, 100, 100] 603
rigid atoms, others: [50, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54])
total number of confs: 1578
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: REAL300025051992 none CCCC(O)(CCC)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 15, 9, 15, 14, 21, 21, 2, 2, 2, 1, 1, 1, 3, 6, 6, 6, 20, 33, 100, 100, 100, 100, 100, 1, 1, 19, 19, 19, 19, 19, 19, 19, 45, 21, 20, 21, 21, 21, 21, 21, 9, 9, 2, 3, 3, 6, 20, 20, 100, 1, 1, 1, 1] 603
rigid atoms, others: [11, 12, 13, 51, 52, 53, 54, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 343
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051992 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051992
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051992/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051992
Building REAL300025051993
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051993'
/scratch/stefan/7786831/working/building/REAL300025051993 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051993

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051993/0 /scratch/stefan/7786831/working/building/REAL300025051993 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 895)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/895
`/scratch/stefan/7786831/working/3D/895' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)CC(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051993.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051993.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051993/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051993 none COC(=O)CC(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 195, 201, 184, 132, 184, 132, 132, 132, 110, 68, 68, 28, 68, 13, 1, 1, 1, 1, 1, 1, 1, 132, 132, 201, 201, 201, 195, 195, 184, 184, 184, 184, 132, 110, 110, 68, 28, 28, 1, 132, 132, 132, 132] 201
rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 878
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051993 none COC(=O)CC(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 26, 11, 26, 7, 2, 7, 2, 2, 1, 1, 1, 4, 7, 7, 7, 24, 45, 132, 132, 132, 132, 132, 1, 1, 26, 26, 26, 11, 11, 7, 7, 7, 7, 2, 4, 4, 7, 24, 24, 132, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 338
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051993 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051993
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051993/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051993
Building REAL300025051994
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051994'
/scratch/stefan/7786831/working/building/REAL300025051994 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051994

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051994/0 /scratch/stefan/7786831/working/building/REAL300025051994 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 896)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/896
`/scratch/stefan/7786831/working/3D/896' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)(C)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051994.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051994.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051994/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051994 none COC(C)(C)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 155, 155, 155, 155, 134, 87, 87, 33, 87, 13, 1, 1, 1, 1, 1, 1, 1, 155, 155, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 155, 134, 134, 87, 33, 33, 1, 155, 155, 155, 155] 201
rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 857
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051994 none COC(C)(C)CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 8, 7, 8, 8, 2, 2, 2, 1, 1, 1, 4, 7, 7, 7, 29, 57, 155, 155, 155, 155, 155, 1, 1, 16, 16, 16, 8, 8, 8, 8, 8, 8, 7, 7, 2, 4, 4, 7, 29, 29, 155, 1, 1, 1, 1] 201
rigid atoms, others: [8, 9, 10, 43, 44, 45, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
total number of confs: 330
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051994 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051994
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051994/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051994
Building REAL300025051995
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051995'
/scratch/stefan/7786831/working/building/REAL300025051995 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051995

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051995/0 /scratch/stefan/7786831/working/building/REAL300025051995 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 897)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/897
`/scratch/stefan/7786831/working/3D/897' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(F)=C(N)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051995.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051995.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051995/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051995 none CC1=CC(F)=C(N)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 15, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 7, 22, 22, 22, 54, 66, 145, 145, 145, 145, 145, 1, 1, 9, 9, 9, 9, 9, 9, 9, 2, 7, 7, 22, 54, 54, 145, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 42, 11, 12, 13, 44, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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])
total number of confs: 353
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051995 none CC1=CC(F)=C(N)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 15, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 32, 71, 71, 71, 124, 135, 201, 201, 201, 201, 201, 9, 9, 2, 2, 2, 1, 1, 1, 1, 9, 32, 32, 71, 124, 124, 201, 9, 9, 9, 9] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 33, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 625
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051995 none CC1=CC(F)=C(N)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 15, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 145, 145, 145, 145, 106, 53, 53, 28, 53, 13, 1, 1, 1, 1, 1, 1, 1, 145, 145, 201, 201, 201, 201, 201, 201, 201, 145, 106, 106, 53, 28, 28, 1, 145, 145, 145, 145] 201
rigid atoms, others: [40, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 642
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051995 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051995
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051995/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051995
Building REAL300025051996
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051996'
/scratch/stefan/7786831/working/building/REAL300025051996 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051996

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051996/0 /scratch/stefan/7786831/working/building/REAL300025051996 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 898)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/898
`/scratch/stefan/7786831/working/3D/898' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCCC(O)C2)CC1)

`REAL300025051996.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051996.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051996/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051996 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCCC(O)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 15, 33, 37, 73, 73, 73, 73, 73, 5, 1, 1, 1, 3, 3, 3, 19, 45, 46, 46, 46, 46, 46, 1, 1, 33, 33, 73, 15, 5, 5, 3, 19, 19, 46, 46, 46, 46, 46, 46, 46, 46, 138, 46, 46, 1, 1, 1, 1] 603
rigid atoms, others: [11, 12, 13, 46, 47, 48, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 477
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051996 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCCC(O)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [34, 22, 13, 1, 1, 1, 1, 1, 1, 1, 34, 34, 61, 73, 73, 73, 73, 164, 200, 201, 201, 201, 201, 201, 73, 73, 22, 22, 1, 34, 61, 61, 73, 164, 164, 201, 201, 201, 201, 201, 201, 201, 201, 603, 201, 201, 73, 73, 73, 73] 603
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 1407
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051996 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCCC(O)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [126, 126, 126, 185, 188, 201, 201, 201, 201, 201, 59, 46, 29, 29, 7, 29, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 185, 185, 201, 126, 59, 59, 29, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 46, 46, 46, 46] 603
rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 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, 43, 46, 47, 48, 49])
total number of confs: 779
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051996 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051996
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051996/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051996
Building REAL300025051997
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051997'
/scratch/stefan/7786831/working/building/REAL300025051997 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051997

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051997/0 /scratch/stefan/7786831/working/building/REAL300025051997 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 899)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/899
`/scratch/stefan/7786831/working/3D/899' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051997.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051997.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051997/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051997 none CC(O)CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 199, 139, 139, 139, 139, 115, 69, 69, 28, 69, 13, 1, 1, 1, 1, 1, 1, 1, 139, 139, 201, 201, 201, 201, 603, 201, 201, 199, 199, 139, 115, 115, 69, 28, 28, 1, 139, 139, 139, 139] 603
rigid atoms, others: [38, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 1472
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: REAL300025051997 none CC(O)CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [16, 11, 16, 9, 2, 2, 2, 1, 1, 1, 4, 7, 7, 7, 26, 43, 139, 139, 139, 139, 139, 1, 1, 16, 16, 16, 16, 48, 12, 12, 9, 9, 2, 4, 4, 7, 26, 26, 139, 1, 1, 1, 1] 603
rigid atoms, others: [39, 8, 9, 42, 7, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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])
total number of confs: 376
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051997 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051997
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051997/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051997
Building REAL300025051998
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051998'
/scratch/stefan/7786831/working/building/REAL300025051998 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051998

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051998/0 /scratch/stefan/7786831/working/building/REAL300025051998 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 900)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/900
`/scratch/stefan/7786831/working/3D/900' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCO1)

`REAL300025051998.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051998.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051998/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051998 none CC1(C)CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 2, 2, 2, 1, 1, 1, 4, 6, 6, 6, 22, 33, 89, 89, 89, 89, 89, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 2, 4, 4, 6, 22, 22, 89, 1, 1, 1, 1, 23, 23, 23, 23] 201
rigid atoms, others: [8, 9, 10, 45, 46, 47, 48, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 44, 49, 50, 51, 52])
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: REAL300025051998 none CC1(C)CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 23, 23, 23, 23, 47, 64, 64, 64, 101, 122, 201, 201, 201, 201, 201, 23, 23, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 23, 47, 47, 64, 101, 101, 201, 23, 23, 23, 23, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 51, 32, 5, 34, 49, 50, 35, 52, 24, 25, 26, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 640
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051998 none CC1(C)CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 179, 89, 89, 89, 89, 79, 48, 48, 23, 48, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 179, 179, 89, 79, 79, 48, 23, 23, 1, 89, 89, 89, 89, 201, 201, 201, 201] 201
rigid atoms, others: [44, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 847
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051998 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051998
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051998/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051998
Building REAL300025051999
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025051999'
/scratch/stefan/7786831/working/building/REAL300025051999 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025051999

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025051999/0 /scratch/stefan/7786831/working/building/REAL300025051999 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 901)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/901
`/scratch/stefan/7786831/working/3D/901' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC=C1C(=O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025051999.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025051999.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025051999/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051999 none CN1C=CC=C1C(=O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 10, 10, 6, 2, 6, 2, 2, 1, 1, 1, 7, 17, 17, 17, 57, 82, 177, 177, 177, 177, 177, 1, 1, 10, 10, 10, 10, 10, 10, 2, 7, 7, 17, 57, 57, 177, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 10, 11, 12, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
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: REAL300025051999 none CN1C=CC=C1C(=O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 23, 38, 38, 38, 91, 116, 201, 201, 201, 201, 201, 10, 10, 2, 2, 2, 1, 1, 1, 10, 23, 23, 38, 91, 91, 201, 10, 10, 10, 10] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29, 30, 31] set([7, 8, 9, 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, 41, 42])
total number of confs: 567
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025051999 none CN1C=CC=C1C(=O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 198, 177, 198, 177, 177, 177, 135, 72, 72, 28, 72, 13, 1, 1, 1, 1, 1, 1, 1, 177, 177, 201, 201, 201, 201, 201, 201, 177, 135, 135, 72, 28, 28, 1, 177, 177, 177, 177] 201
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42])
total number of confs: 755
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025051999 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025051999
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025051999/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025051999
Building REAL300025052000
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052000'
/scratch/stefan/7786831/working/building/REAL300025052000 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052000

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052000/0 /scratch/stefan/7786831/working/building/REAL300025052000 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 902)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/902
`/scratch/stefan/7786831/working/3D/902' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCS(O)=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052000.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052000.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052000/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
Warning: Using closest atom type 60 for atom 3
Warning: Using closest atom type 60 for atom 3
('energy: ', 12.0)
('conf: ', 200)
Warning: Using closest atom type 60 for atom 3
Warning: Using closest atom type 60 for atom 3
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052000 none CCS(O)=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.3', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 14, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 182, 182, 182, 182, 143, 71, 71, 30, 71, 13, 1, 1, 1, 1, 1, 1, 1, 182, 182, 201, 201, 201, 201, 201, 201, 201, 182, 143, 143, 71, 30, 30, 1, 182, 182, 182, 182] 201
rigid atoms, others: [36, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
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: REAL300025052000 none CCS(O)=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.3', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 14, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 6, 6, 6, 2, 2, 2, 1, 1, 1, 7, 18, 18, 18, 44, 64, 182, 182, 182, 182, 182, 1, 1, 11, 11, 11, 11, 11, 6, 6, 2, 7, 7, 18, 44, 44, 182, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 7, 8, 9, 39, 40, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 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])
total number of confs: 412
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052000 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052000
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052000/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052000
Building REAL300025052001
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052001'
/scratch/stefan/7786831/working/building/REAL300025052001 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052001

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052001/0 /scratch/stefan/7786831/working/building/REAL300025052001 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 903)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/903
`/scratch/stefan/7786831/working/3D/903' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)C1=CNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025052001.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052001.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052001/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052001 none CC(=O)C1=CNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 11, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 4, 12, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 22, 22, 22, 66, 88, 186, 186, 186, 186, 186, 1, 1, 4, 12, 12, 12, 4, 4, 2, 7, 7, 22, 66, 66, 186, 1, 1, 1, 1, 4] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42])
total number of confs: 476
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052001 none CC(=O)C1=CNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 11, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 30, 30, 30, 82, 106, 189, 189, 189, 189, 189, 4, 4, 1, 7, 7, 7, 1, 1, 4, 11, 11, 30, 82, 82, 189, 4, 4, 4, 4, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 42, 25, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 525
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052001 none CC(=O)C1=CNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 11, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 189, 201, 189, 189, 189, 186, 186, 186, 186, 132, 57, 57, 29, 57, 13, 1, 1, 1, 1, 1, 1, 1, 186, 186, 189, 201, 201, 201, 189, 189, 186, 132, 132, 57, 29, 29, 1, 186, 186, 186, 186, 189] 201
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 759
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052001 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052001
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052001/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052001
Building REAL300025052002
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052002'
/scratch/stefan/7786831/working/building/REAL300025052002 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052002

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052002/0 /scratch/stefan/7786831/working/building/REAL300025052002 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 904)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/904
`/scratch/stefan/7786831/working/3D/904' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)NCCCCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052002.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052002.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052002/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052002 none NC(=O)NCCCCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 184, 158, 160, 158, 141, 77, 77, 77, 77, 69, 54, 54, 42, 54, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 201, 201, 201, 183, 184, 160, 160, 160, 160, 160, 160, 141, 141, 77, 69, 69, 54, 42, 42, 1, 77, 77, 77, 77] 201
rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50])
total number of confs: 902
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052002 none NC(=O)NCCCCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [34, 34, 34, 22, 13, 14, 13, 10, 2, 2, 2, 1, 1, 1, 3, 7, 7, 7, 24, 35, 77, 77, 77, 77, 77, 1, 1, 34, 34, 34, 22, 23, 14, 14, 14, 14, 14, 14, 10, 10, 2, 3, 3, 7, 24, 24, 77, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 47, 48, 49, 50, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 320
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052002 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052002
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052002/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052002
Building REAL300025052003
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052003'
/scratch/stefan/7786831/working/building/REAL300025052003 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052003

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052003/0 /scratch/stefan/7786831/working/building/REAL300025052003 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 905)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/905
`/scratch/stefan/7786831/working/3D/905' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CC=C(O)C=C2)CC1)

`REAL300025052003.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052003.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052003/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052003 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CC=C(O)C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 19, 64, 80, 151, 151, 151, 151, 151, 5, 1, 1, 1, 3, 3, 3, 8, 12, 12, 8, 12, 12, 12, 1, 1, 64, 64, 151, 19, 5, 5, 3, 8, 8, 12, 12, 24, 12, 12, 1, 1, 1, 1] 402
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 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: REAL300025052003 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CC=C(O)C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [74, 32, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 132, 151, 151, 151, 151, 201, 201, 201, 201, 201, 201, 201, 151, 151, 32, 32, 1, 74, 132, 132, 151, 201, 201, 201, 201, 402, 201, 201, 151, 151, 151, 151] 402
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 1230
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052003 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CC=C(O)C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [60, 60, 60, 141, 158, 201, 201, 201, 201, 201, 22, 12, 8, 8, 4, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 141, 141, 201, 60, 22, 22, 8, 4, 4, 1, 1, 2, 1, 1, 12, 12, 12, 12] 402
rigid atoms, others: [35, 36, 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, 37, 40, 41, 42, 43])
total number of confs: 671
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052003 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052003
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052003/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052003
Building REAL300025052004
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052004'
/scratch/stefan/7786831/working/building/REAL300025052004 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052004

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052004/0 /scratch/stefan/7786831/working/building/REAL300025052004 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 906)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/906
`/scratch/stefan/7786831/working/3D/906' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=C1[N+](=O)[O-])

`REAL300025052004.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052004.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052004/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052004 none CN1C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 8, 11, 11, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 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: [7, 7, 2, 2, 2, 1, 1, 1, 7, 28, 28, 28, 59, 67, 140, 140, 140, 140, 140, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 7, 7, 28, 59, 59, 140, 1, 1, 1, 1, 7, 7] 201
rigid atoms, others: [37, 6, 7, 40, 39, 19, 20, 38, 5] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42])
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: REAL300025052004 none CN1C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 8, 11, 11, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 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: [1, 1, 1, 1, 7, 7, 7, 7, 23, 60, 60, 60, 107, 116, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 2, 2, 2, 2, 2, 7, 23, 23, 60, 107, 107, 201, 7, 7, 7, 7, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 41, 42, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 580
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052004 none CN1C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 8, 11, 11, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 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: [201, 201, 140, 140, 140, 140, 92, 45, 45, 27, 45, 13, 1, 1, 1, 1, 1, 1, 1, 140, 140, 201, 201, 201, 201, 201, 201, 201, 201, 201, 140, 92, 92, 45, 27, 27, 1, 140, 140, 140, 140, 201, 201] 201
rigid atoms, others: [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, 34, 35, 37, 38, 39, 40, 41, 42])
total number of confs: 646
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052004 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052004
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052004/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052004
Building REAL300025052005
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052005'
/scratch/stefan/7786831/working/building/REAL300025052005 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052005

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052005/0 /scratch/stefan/7786831/working/building/REAL300025052005 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 907)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/907
`/scratch/stefan/7786831/working/3D/907' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=CC=C1)

`REAL300025052005.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052005.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052005/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052005 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 169, 169, 169, 169, 130, 50, 50, 28, 50, 12, 1, 1, 1, 1, 1, 1, 1, 169, 169, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 169, 130, 130, 50, 28, 28, 1, 169, 169, 169, 169, 201, 201, 201, 201, 201] 201
rigid atoms, others: [36, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 846
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052005 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 2, 2, 2, 1, 1, 1, 6, 23, 23, 23, 68, 83, 169, 169, 169, 169, 169, 1, 1, 4, 6, 6, 4, 6, 6, 4, 4, 4, 4, 2, 6, 6, 23, 68, 68, 169, 1, 1, 1, 1, 6, 6, 6, 6, 6] 201
rigid atoms, others: [4, 5, 6, 39, 40, 18, 19, 38, 37] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45])
total number of confs: 434
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052005 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 6, 6, 6, 6, 14, 46, 46, 46, 108, 125, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 14, 14, 46, 108, 108, 201, 6, 6, 6, 6, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 41, 42, 43, 44, 45, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 576
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052005 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052005
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052005/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052005
Building REAL300025052006
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052006'
/scratch/stefan/7786831/working/building/REAL300025052006 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025052006

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052006/0 /scratch/stefan/7786831/working/building/REAL300025052006 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 908)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/908
`/scratch/stefan/7786831/working/3D/908' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C[N-]C(=O)C(F)(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052006.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052006.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052006/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052006 none O=C(C[N-]C(=O)C(F)(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.2', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 15, 15, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [110, 110, 110, 182, 198, 201, 201, 201, 201, 201, 110, 97, 74, 74, 32, 74, 13, 1, 1, 1, 1, 1, 1, 1, 110, 110, 182, 182, 110, 97, 97, 74, 32, 32, 1, 110, 110, 110, 110] 201
rigid atoms, others: [34, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 811
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052006 none O=C(C[N-]C(=O)C(F)(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.2', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 15, 15, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 6, 16, 28, 28, 28, 28, 28, 1, 1, 1, 4, 10, 10, 10, 25, 42, 110, 110, 110, 110, 110, 1, 1, 6, 6, 2, 4, 4, 10, 25, 25, 110, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 10, 11, 12, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 279
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052006 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025052006/1 /scratch/stefan/7786831/working/building/REAL300025052006 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 909)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/909
`/scratch/stefan/7786831/working/3D/909' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CNC(=O)C(F)(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052006.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025052006.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052006/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052006 none O=C(CNC(=O)C(F)(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 15, 15, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [96, 96, 96, 190, 201, 201, 201, 201, 201, 201, 96, 77, 44, 44, 28, 44, 13, 1, 1, 1, 1, 1, 1, 1, 96, 96, 190, 190, 201, 96, 77, 77, 44, 28, 28, 1, 96, 96, 96, 96] 201
rigid atoms, others: [35, 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, 36, 37, 38, 39])
total number of confs: 827
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052006 none O=C(CNC(=O)C(F)(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 15, 15, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 12, 24, 24, 24, 24, 24, 24, 1, 1, 1, 6, 12, 12, 12, 26, 37, 96, 96, 96, 96, 96, 1, 1, 12, 12, 24, 2, 6, 6, 12, 26, 26, 96, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 274
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052006 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052006
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025052006/1.*
0: /scratch/stefan/7786831/working/building/REAL300025052006/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052006
Building REAL300025052007
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052007'
/scratch/stefan/7786831/working/building/REAL300025052007 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052007

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052007/0 /scratch/stefan/7786831/working/building/REAL300025052007 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 910)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/910
`/scratch/stefan/7786831/working/3D/910' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=NC([O-])=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1)

`REAL300025052007.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052007.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052007/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052007 none NC1=NC([O-])=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'N.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 8, 1, 12, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 6, 6, 6, 2, 2, 2, 1, 1, 1, 7, 17, 17, 17, 49, 82, 149, 149, 149, 149, 149, 1, 1, 6, 6, 6, 6, 6, 2, 7, 7, 17, 49, 49, 149, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 368
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052007 none NC1=NC([O-])=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'N.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 8, 1, 12, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 6, 20, 44, 44, 44, 100, 151, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 3, 3, 6, 20, 20, 44, 100, 100, 201, 6, 6, 6, 6] 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, 40])
total number of confs: 567
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052007 none NC1=NC([O-])=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)S1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'N.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 8, 1, 12, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 149, 149, 149, 149, 126, 91, 91, 33, 91, 13, 1, 1, 1, 1, 1, 1, 1, 149, 149, 201, 201, 201, 201, 201, 149, 126, 126, 91, 33, 33, 1, 149, 149, 149, 149] 201
rigid atoms, others: [36, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 794
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052007 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052007
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052007/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052007
Building REAL300025052008
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052008'
/scratch/stefan/7786831/working/building/REAL300025052008 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052008

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052008/0 /scratch/stefan/7786831/working/building/REAL300025052008 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 911)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/911
`/scratch/stefan/7786831/working/3D/911' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1O)

`REAL300025052008.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052008.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052008/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052008 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
304  conformations in input
total number of sets (complete confs): 304
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 19, 19, 19, 56, 67, 101, 101, 101, 101, 101, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 19, 56, 56, 101, 1, 1, 1, 1, 5, 10] 304
rigid atoms, others: [38, 7, 8, 9, 39, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 42, 43])
total number of confs: 308
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052008 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
304  conformations in input
total number of sets (complete confs): 304
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 56, 56, 56, 113, 126, 152, 152, 152, 152, 152, 5, 5, 1, 1, 1, 2, 2, 2, 1, 1, 5, 13, 13, 56, 113, 113, 152, 5, 5, 5, 5, 1, 2] 304
rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 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, 43])
total number of confs: 520
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052008 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
304  conformations in input
total number of sets (complete confs): 304
using faster count positions algorithm for large data
unique positions, atoms: [152, 152, 152, 152, 101, 101, 101, 101, 83, 55, 55, 24, 55, 13, 1, 1, 1, 1, 1, 1, 1, 101, 101, 152, 152, 152, 152, 152, 152, 152, 152, 101, 83, 83, 55, 24, 24, 1, 101, 101, 101, 101, 152, 304] 304
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43])
total number of confs: 757
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052008 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052008
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052008/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052008
Building REAL300025052009
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052009'
/scratch/stefan/7786831/working/building/REAL300025052009 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052009

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052009/0 /scratch/stefan/7786831/working/building/REAL300025052009 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 912)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/912
`/scratch/stefan/7786831/working/3D/912' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(COCC(F)(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052009.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052009.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052009/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052009 none O=C(COCC(F)(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 5, 5, 15, 15, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [106, 106, 106, 191, 197, 201, 201, 201, 201, 106, 84, 54, 54, 29, 54, 13, 1, 1, 1, 1, 1, 1, 1, 106, 106, 191, 191, 201, 201, 106, 84, 84, 54, 29, 29, 1, 106, 106, 106, 106] 201
rigid atoms, others: [35, 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, 36, 37, 38, 39])
total number of confs: 854
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052009 none O=C(COCC(F)(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 5, 5, 15, 15, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 7, 16, 35, 35, 35, 35, 1, 1, 1, 4, 6, 6, 6, 21, 33, 106, 106, 106, 106, 106, 1, 1, 7, 7, 35, 35, 2, 4, 4, 6, 21, 21, 106, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 330
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052009 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052009
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052009/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052009
Building REAL300025052010
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052010'
/scratch/stefan/7786831/working/building/REAL300025052010 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052010

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052010/0 /scratch/stefan/7786831/working/building/REAL300025052010 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 913)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/913
`/scratch/stefan/7786831/working/3D/913' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(Cl)=N1)

`REAL300025052010.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052010.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052010/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052010 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(Cl)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
153  conformations in input
total number of sets (complete confs): 153
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 4, 21, 21, 21, 72, 90, 125, 125, 125, 125, 125, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 2, 4, 4, 21, 72, 72, 125, 1, 1, 1, 1] 153
rigid atoms, others: [38, 7, 8, 9, 39, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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])
total number of confs: 362
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052010 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(Cl)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 17, 54, 54, 54, 111, 126, 153, 153, 153, 153, 153, 7, 7, 1, 1, 1, 2, 2, 2, 1, 1, 7, 17, 17, 54, 111, 111, 153, 7, 7, 7, 7] 153
rigid atoms, others: [0, 1, 2, 3, 4, 5, 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])
total number of confs: 510
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052010 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(Cl)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
153  conformations in input
total number of sets (complete confs): 153
using faster count positions algorithm for large data
unique positions, atoms: [153, 153, 153, 153, 125, 125, 125, 125, 104, 63, 63, 21, 63, 12, 1, 1, 1, 1, 1, 1, 1, 125, 125, 153, 153, 153, 153, 153, 153, 153, 153, 125, 104, 104, 63, 21, 21, 1, 125, 125, 125, 125] 153
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41])
total number of confs: 498
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052010 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052010
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052010/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052010
Building REAL300025052011
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052011'
/scratch/stefan/7786831/working/building/REAL300025052011 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052011

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052011/0 /scratch/stefan/7786831/working/building/REAL300025052011 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 914)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/914
`/scratch/stefan/7786831/working/3D/914' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=C1F)

`REAL300025052011.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052011.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052011/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052011 none NC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=C1F NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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: [8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 15, 6, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 2, 2, 1, 1, 1, 4, 19, 19, 19, 55, 62, 105, 105, 105, 105, 105, 1, 1, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 19, 55, 55, 105, 1, 1, 1, 1, 5, 5] 201
rigid atoms, others: [36, 37, 6, 7, 8, 39, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 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, 40, 41])
total number of confs: 300
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052011 none NC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=C1F NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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: [8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 15, 6, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 5, 5, 5, 5, 13, 64, 64, 64, 138, 156, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 1, 2, 2, 1, 5, 13, 13, 64, 138, 138, 201, 5, 5, 5, 5, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 40, 41, 22, 23, 24, 25, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 648
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052011 none NC1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=C1F NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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: [8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 15, 6, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 105, 105, 105, 105, 87, 57, 57, 25, 57, 13, 1, 1, 1, 1, 1, 1, 1, 105, 105, 201, 201, 201, 201, 201, 201, 201, 105, 87, 87, 57, 25, 25, 1, 105, 105, 105, 105, 201, 201] 201
rigid atoms, others: [35, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41])
total number of confs: 544
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052011 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052011
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052011/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052011
Building REAL300025052012
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052012'
/scratch/stefan/7786831/working/building/REAL300025052012 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052012

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052012/0 /scratch/stefan/7786831/working/building/REAL300025052012 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 915)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/915
`/scratch/stefan/7786831/working/3D/915' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)CSCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052012.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052012.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052012/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052012 none NC(=O)CSCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [8, 1, 11, 5, 14, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 194, 133, 133, 133, 133, 114, 86, 86, 30, 86, 13, 1, 1, 1, 1, 1, 1, 1, 133, 133, 201, 201, 201, 201, 194, 194, 133, 114, 114, 86, 30, 30, 1, 133, 133, 133, 133] 201
rigid atoms, others: [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, 34, 35, 37, 38, 39, 40])
total number of confs: 813
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052012 none NC(=O)CSCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [8, 1, 11, 5, 14, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 16, 20, 15, 7, 2, 2, 2, 1, 1, 1, 4, 10, 10, 10, 29, 56, 133, 133, 133, 133, 133, 1, 1, 20, 20, 16, 16, 7, 7, 2, 4, 4, 10, 29, 29, 133, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 40, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 322
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052012 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052012
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052012/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052012
Building REAL300025052013
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052013'
/scratch/stefan/7786831/working/building/REAL300025052013 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052013

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052013/0 /scratch/stefan/7786831/working/building/REAL300025052013 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 916)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/916
`/scratch/stefan/7786831/working/3D/916' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCSCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052013.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052013.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052013/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052013 none CCCCSCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 14, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 150, 139, 103, 103, 103, 103, 89, 73, 73, 50, 73, 13, 1, 1, 1, 1, 1, 1, 1, 103, 103, 201, 201, 201, 201, 201, 201, 201, 201, 201, 139, 139, 103, 89, 89, 73, 50, 50, 1, 103, 103, 103, 103] 201
rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 904
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052013 none CCCCSCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 14, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 31, 31, 11, 7, 2, 2, 2, 1, 1, 1, 3, 5, 5, 5, 24, 40, 103, 103, 103, 103, 103, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 7, 7, 2, 3, 3, 5, 24, 24, 103, 1, 1, 1, 1] 201
rigid atoms, others: [8, 9, 10, 43, 44, 45, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
total number of confs: 326
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052013 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052013
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052013/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052013
Building REAL300025052014
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052014'
/scratch/stefan/7786831/working/building/REAL300025052014 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052014

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052014/0 /scratch/stefan/7786831/working/building/REAL300025052014 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 917)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/917
`/scratch/stefan/7786831/working/3D/917' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025052014.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052014.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052014/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052014 none NC1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 20, 20, 20, 75, 93, 156, 156, 156, 156, 156, 1, 1, 5, 5, 5, 5, 5, 2, 4, 4, 20, 75, 75, 156, 1, 1, 1, 1, 5] 201
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40])
total number of confs: 414
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052014 none NC1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 50, 50, 50, 132, 156, 201, 201, 201, 201, 201, 5, 5, 1, 2, 2, 1, 1, 5, 13, 13, 50, 132, 132, 201, 5, 5, 5, 5, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 40, 24, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 627
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052014 none NC1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 156, 156, 156, 156, 130, 78, 78, 33, 78, 13, 1, 1, 1, 1, 1, 1, 1, 156, 156, 201, 201, 201, 201, 201, 156, 130, 130, 78, 33, 33, 1, 156, 156, 156, 156, 201] 201
rigid atoms, others: [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, 33, 34, 36, 37, 38, 39, 40])
total number of confs: 667
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052014 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052014
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052014/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052014
Building REAL300025052015
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052015'
/scratch/stefan/7786831/working/building/REAL300025052015 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052015

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052015/0 /scratch/stefan/7786831/working/building/REAL300025052015 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 918)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/918
`/scratch/stefan/7786831/working/3D/918' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1)

`REAL300025052015.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052015.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052015/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052015 none CC1=CC=C(C(=O)C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 15, 15, 6, 2, 6, 2, 2, 1, 1, 1, 7, 16, 16, 16, 45, 71, 164, 164, 164, 164, 164, 1, 1, 15, 15, 15, 15, 15, 15, 15, 2, 7, 7, 16, 45, 45, 164, 1, 1, 1, 1, 15, 15] 201
rigid atoms, others: [39, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44])
total number of confs: 429
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052015 none CC1=CC=C(C(=O)C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 11, 11, 11, 11, 21, 35, 35, 35, 90, 125, 201, 201, 201, 201, 201, 11, 11, 1, 1, 2, 2, 2, 1, 1, 11, 21, 21, 35, 90, 90, 201, 11, 11, 11, 11, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 44, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 560
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052015 none CC1=CC=C(C(=O)C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 164, 199, 164, 164, 164, 123, 67, 67, 29, 67, 13, 1, 1, 1, 1, 1, 1, 1, 164, 164, 201, 201, 201, 201, 201, 201, 201, 164, 123, 123, 67, 29, 29, 1, 164, 164, 164, 164, 201, 201] 201
rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44])
total number of confs: 756
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052015 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052015
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052015/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052015
Building REAL300025052016
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052016'
/scratch/stefan/7786831/working/building/REAL300025052016 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052016

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052016/0 /scratch/stefan/7786831/working/building/REAL300025052016 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 919)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/919
`/scratch/stefan/7786831/working/3D/919' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CSCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052016.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052016.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052016/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052016 none CC(C)CSCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 14, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 170, 158, 96, 96, 96, 96, 81, 55, 55, 27, 55, 13, 1, 1, 1, 1, 1, 1, 1, 96, 96, 201, 201, 201, 201, 201, 201, 201, 201, 201, 158, 158, 96, 81, 81, 55, 27, 27, 1, 96, 96, 96, 96] 201
rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 895
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052016 none CC(C)CSCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 14, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [37, 37, 37, 13, 7, 2, 2, 2, 1, 1, 1, 3, 5, 5, 5, 16, 29, 96, 96, 96, 96, 96, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 37, 7, 7, 2, 3, 3, 5, 16, 16, 96, 1, 1, 1, 1] 201
rigid atoms, others: [8, 9, 10, 43, 44, 45, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
total number of confs: 316
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052016 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052016
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052016/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052016
Building REAL300025052017
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052017'
/scratch/stefan/7786831/working/building/REAL300025052017 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052017

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052017/0 /scratch/stefan/7786831/working/building/REAL300025052017 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 920)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/920
`/scratch/stefan/7786831/working/3D/920' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1CCCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052017.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052017.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052017/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052017 none CC(=O)N1CCCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 5, 6, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 7, 20, 20, 20, 63, 88, 170, 170, 170, 170, 170, 1, 1, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 7, 7, 20, 63, 63, 170, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 46, 47, 48, 49, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 433
number of broken/clashed sets: 188
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052017 none CC(=O)N1CCCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 15, 37, 37, 37, 99, 126, 201, 201, 201, 201, 201, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 37, 99, 99, 201, 5, 5, 5, 5] 201
rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 8, 9, 7, 35, 36, 38, 37, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 580
number of broken/clashed sets: 188
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052017 none CC(=O)N1CCCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 170, 170, 170, 170, 141, 76, 76, 31, 76, 13, 1, 1, 1, 1, 1, 1, 1, 170, 170, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 170, 141, 141, 76, 31, 31, 1, 170, 170, 170, 170] 201
rigid atoms, others: [45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49])
total number of confs: 765
number of broken/clashed sets: 188
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052017 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052017
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052017/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052017
Building REAL300025052018
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052018'
/scratch/stefan/7786831/working/building/REAL300025052018 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052018

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052018/0 /scratch/stefan/7786831/working/building/REAL300025052018 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 921)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/921
`/scratch/stefan/7786831/working/3D/921' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(=O)NC(=O)N2)CC1)

`REAL300025052018.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052018.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052018/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052018 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(=O)NC(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 18, 57, 66, 125, 125, 125, 125, 125, 5, 1, 1, 1, 3, 3, 3, 16, 16, 16, 16, 16, 16, 16, 1, 1, 57, 57, 125, 18, 5, 5, 3, 16, 16, 16, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
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: REAL300025052018 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(=O)NC(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [67, 32, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 103, 125, 125, 125, 125, 201, 201, 201, 201, 201, 201, 201, 125, 125, 32, 32, 1, 67, 103, 103, 125, 201, 201, 201, 125, 125, 125, 125] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 580
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052018 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(=O)NC(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 1, 11, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [77, 77, 77, 150, 169, 201, 201, 201, 201, 201, 25, 16, 10, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 150, 150, 201, 77, 25, 25, 10, 1, 1, 1, 16, 16, 16, 16] 201
rigid atoms, others: [33, 34, 35, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39])
total number of confs: 677
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052018 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052018
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052018/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052018
Building REAL300025052019
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052019'
/scratch/stefan/7786831/working/building/REAL300025052019 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025052019

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052019/0 /scratch/stefan/7786831/working/building/REAL300025052019 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 922)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/922
`/scratch/stefan/7786831/working/3D/922' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2C[N@@H+]3CCN2CCC3)CC1)

`REAL300025052019.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052019.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052019/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052019 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2C[N@@H+]3CCN2CCC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 9, 6, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [9, 9, 9, 24, 29, 32, 32, 32, 32, 32, 4, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 24, 24, 32, 9, 4, 4, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1] 32
rigid atoms, others: [11, 12, 13, 48, 49, 50, 51, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 119
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: REAL300025052019 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2C[N@@H+]3CCN2CCC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 9, 6, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [28, 18, 13, 1, 1, 1, 1, 1, 1, 1, 28, 28, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 18, 18, 1, 28, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 32
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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, 46, 47, 48, 49, 50, 51])
total number of confs: 99
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052019 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2C[N@@H+]3CCN2CCC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 9, 6, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [11, 11, 11, 26, 31, 32, 32, 32, 32, 32, 6, 5, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 26, 26, 32, 11, 6, 6, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 32
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 48, 49, 50, 51])
total number of confs: 115
number of broken/clashed sets: 32
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052019 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025052019/1 /scratch/stefan/7786831/working/building/REAL300025052019 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 923)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/923
`/scratch/stefan/7786831/working/3D/923' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2C[N@H+]3CCN2CCC3)CC1)

`REAL300025052019.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025052019.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052019/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052019 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2C[N@H+]3CCN2CCC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 9, 6, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [15, 15, 15, 23, 25, 29, 29, 29, 29, 29, 5, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 23, 23, 29, 15, 5, 5, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1] 30
rigid atoms, others: [11, 12, 13, 48, 49, 50, 51, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 111
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052019 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2C[N@H+]3CCN2CCC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 9, 6, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [25, 18, 12, 1, 1, 1, 1, 1, 1, 1, 25, 25, 29, 29, 29, 29, 29, 30, 30, 30, 30, 30, 30, 30, 30, 30, 29, 29, 18, 18, 1, 25, 29, 29, 29, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 29, 29, 29, 29] 30
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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, 46, 47, 48, 49, 50, 51])
total number of confs: 93
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052019 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2C[N@H+]3CCN2CCC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 9, 6, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [18, 18, 18, 25, 27, 30, 30, 30, 30, 30, 10, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 30, 18, 10, 10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 30
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 48, 49, 50, 51])
total number of confs: 114
number of broken/clashed sets: 30
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052019 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052019
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025052019/1.*
0: /scratch/stefan/7786831/working/building/REAL300025052019/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052019
Building REAL300025052020
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052020'
/scratch/stefan/7786831/working/building/REAL300025052020 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052020

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052020/0 /scratch/stefan/7786831/working/building/REAL300025052020 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 924)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/924
`/scratch/stefan/7786831/working/3D/924' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CNC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1=O)

`REAL300025052020.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052020.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052020/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052020 none CC1=CNC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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: [5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 7, 29, 29, 29, 88, 113, 197, 199, 199, 199, 199, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 2, 7, 7, 29, 88, 88, 199, 1, 1, 1, 1] 201
rigid atoms, others: [39, 8, 9, 10, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 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: REAL300025052020 none CC1=CNC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 40, 40, 40, 110, 132, 199, 201, 201, 201, 201, 5, 5, 1, 1, 2, 2, 2, 1, 1, 1, 5, 13, 13, 40, 110, 110, 201, 5, 5, 5, 5] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 25, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 602
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052020 none CC1=CNC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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, 199, 199, 199, 199, 140, 67, 67, 29, 67, 13, 1, 1, 1, 1, 1, 1, 1, 199, 199, 201, 201, 201, 201, 201, 201, 201, 201, 199, 140, 140, 67, 29, 29, 1, 199, 199, 199, 199] 201
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42])
total number of confs: 741
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052020 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052020
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052020/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052020
Building REAL300025052021
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052021'
/scratch/stefan/7786831/working/building/REAL300025052021 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052021

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052021/0 /scratch/stefan/7786831/working/building/REAL300025052021 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 925)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/925
`/scratch/stefan/7786831/working/3D/925' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C=CC=C2)CC1)

`REAL300025052021.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052021.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052021/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052021 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C=CC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 17, 37, 47, 141, 141, 141, 141, 141, 5, 1, 1, 1, 3, 3, 3, 19, 28, 28, 28, 28, 1, 1, 37, 37, 141, 17, 5, 5, 3, 19, 19, 28, 28, 28, 28, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
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: REAL300025052021 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C=CC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [71, 33, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 118, 141, 141, 141, 141, 201, 201, 201, 201, 201, 141, 141, 33, 33, 1, 71, 118, 118, 141, 201, 201, 201, 201, 201, 201, 141, 141, 141, 141] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 846
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052021 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2C=CC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [78, 78, 78, 127, 142, 201, 201, 201, 201, 201, 41, 29, 21, 21, 5, 21, 1, 1, 1, 1, 1, 1, 29, 29, 127, 127, 201, 78, 41, 41, 21, 5, 5, 1, 1, 1, 1, 29, 29, 29, 29] 201
rigid atoms, others: [33, 34, 35, 36, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40])
total number of confs: 657
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052021 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052021
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052021/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052021
Building REAL300025052022
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052022'
/scratch/stefan/7786831/working/building/REAL300025052022 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052022

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052022/0 /scratch/stefan/7786831/working/building/REAL300025052022 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 926)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/926
`/scratch/stefan/7786831/working/3D/926' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCCS2)CC1)

`REAL300025052022.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052022.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052022/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052022 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCCS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 20, 63, 79, 161, 161, 161, 161, 161, 6, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 1, 1, 63, 63, 161, 20, 6, 6, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
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: REAL300025052022 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCCS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [75, 36, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 136, 161, 161, 161, 161, 201, 201, 201, 201, 201, 161, 161, 36, 36, 1, 75, 136, 136, 161, 201, 201, 201, 201, 201, 201, 201, 201, 201, 161, 161, 161, 161] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 770
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052022 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCCS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [60, 60, 60, 125, 139, 201, 201, 201, 201, 201, 24, 14, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 125, 125, 201, 60, 24, 24, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43])
total number of confs: 645
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052022 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052022
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052022/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052022
Building REAL300025052023
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052023'
/scratch/stefan/7786831/working/building/REAL300025052023 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052023

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052023/0 /scratch/stefan/7786831/working/building/REAL300025052023 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 927)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/927
`/scratch/stefan/7786831/working/3D/927' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2SCCS2)CC1)

`REAL300025052023.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052023.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052023/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052023 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2SCCS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 14, 5, 5, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 20, 75, 93, 165, 165, 165, 165, 165, 5, 1, 1, 1, 3, 3, 3, 16, 16, 16, 16, 1, 1, 75, 75, 165, 20, 5, 5, 3, 16, 16, 16, 16, 16, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 455
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052023 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2SCCS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 14, 5, 5, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [82, 33, 13, 1, 1, 1, 1, 1, 1, 1, 82, 82, 146, 165, 165, 165, 165, 201, 201, 201, 201, 165, 165, 33, 33, 1, 82, 146, 146, 165, 201, 201, 201, 201, 201, 165, 165, 165, 165] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 25] set([0, 1, 2, 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: 753
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052023 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2SCCS2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 14, 5, 5, 14, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [75, 75, 75, 150, 162, 201, 201, 201, 201, 201, 27, 16, 11, 11, 1, 11, 1, 1, 1, 1, 1, 16, 16, 150, 150, 201, 75, 27, 27, 11, 1, 1, 1, 1, 1, 16, 16, 16, 16] 201
rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38])
total number of confs: 687
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052023 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052023
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052023/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052023
Building REAL300025052024
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052024'
/scratch/stefan/7786831/working/building/REAL300025052024 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052024

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052024/0 /scratch/stefan/7786831/working/building/REAL300025052024 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 928)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/928
`/scratch/stefan/7786831/working/3D/928' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=N1)

`REAL300025052024.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052024.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052024/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052024 none NC(=O)C1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=N1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 6, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 6, 23, 23, 23, 83, 105, 141, 141, 141, 141, 141, 1, 1, 5, 5, 5, 5, 5, 5, 2, 6, 6, 23, 83, 83, 141, 1, 1, 1, 1, 5, 5] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 40, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42])
total number of confs: 410
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052024 none NC(=O)C1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=N1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 6, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 15, 62, 62, 62, 145, 170, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 2, 2, 1, 5, 15, 15, 62, 145, 145, 201, 5, 5, 5, 5, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 42, 24, 25, 26, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 642
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052024 none NC(=O)C1=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=CC=N1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 6, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 141, 141, 141, 141, 114, 63, 63, 24, 63, 12, 1, 1, 1, 1, 1, 1, 1, 141, 141, 201, 201, 201, 201, 201, 201, 141, 114, 114, 63, 24, 24, 1, 141, 141, 141, 141, 201, 201] 201
rigid atoms, others: [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, 34, 35, 37, 38, 39, 40, 41, 42])
total number of confs: 629
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052024 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052024
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052024/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052024
Building REAL300025052025
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052025'
/scratch/stefan/7786831/working/building/REAL300025052025 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025052025

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052025/0 /scratch/stefan/7786831/working/building/REAL300025052025 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 929)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/929
`/scratch/stefan/7786831/working/3D/929' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(O)C=C2F)CC1)

`REAL300025052025.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052025.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052025/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052025 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(O)C=C2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [28, 28, 28, 88, 98, 187, 187, 187, 187, 187, 6, 1, 1, 1, 3, 3, 3, 10, 10, 5, 10, 10, 10, 10, 1, 1, 88, 88, 187, 28, 6, 6, 3, 10, 10, 20, 10, 1, 1, 1, 1] 402
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 525
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052025 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(O)C=C2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [59, 31, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 132, 187, 187, 187, 187, 201, 201, 201, 201, 201, 201, 201, 187, 187, 31, 31, 1, 59, 132, 132, 187, 201, 201, 402, 201, 187, 187, 187, 187] 402
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 1133
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052025 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(O)C=C2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [59, 59, 59, 136, 142, 201, 201, 201, 201, 201, 17, 10, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 136, 136, 201, 59, 17, 17, 7, 1, 1, 2, 1, 10, 10, 10, 10] 402
rigid atoms, others: [33, 34, 36, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 37, 38, 39, 40])
total number of confs: 637
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052025 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025052025/1 /scratch/stefan/7786831/working/building/REAL300025052025 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 930)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/930
`/scratch/stefan/7786831/working/3D/930' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C([O-])C=C2F)CC1)

`REAL300025052025.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025052025.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052025/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052025 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C([O-])C=C2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 65, 106, 180, 180, 180, 180, 180, 6, 1, 1, 1, 3, 3, 3, 11, 11, 3, 11, 11, 11, 11, 1, 1, 65, 65, 180, 22, 6, 6, 3, 11, 11, 11, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
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: REAL300025052025 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C([O-])C=C2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [94, 39, 13, 1, 1, 1, 1, 1, 1, 1, 94, 94, 158, 180, 180, 180, 180, 201, 201, 180, 201, 201, 201, 201, 180, 180, 39, 39, 1, 94, 158, 158, 180, 201, 201, 201, 180, 180, 180, 180] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 839
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052025 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C([O-])C=C2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [52, 52, 52, 112, 154, 201, 201, 201, 201, 201, 22, 11, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 112, 112, 201, 52, 22, 22, 6, 1, 1, 1, 11, 11, 11, 11] 201
rigid atoms, others: [33, 34, 35, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39])
total number of confs: 599
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052025 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052025
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025052025/1.*
0: /scratch/stefan/7786831/working/building/REAL300025052025/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052025
Building REAL300025052026
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052026'
/scratch/stefan/7786831/working/building/REAL300025052026 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052026

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052026/0 /scratch/stefan/7786831/working/building/REAL300025052026 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 931)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/931
`/scratch/stefan/7786831/working/3D/931' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NN(CO)C=C2)CC1)

`REAL300025052026.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052026.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052026/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052026 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NN(CO)C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 8, 5, 12, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [21, 21, 21, 60, 68, 160, 160, 160, 160, 160, 5, 1, 1, 1, 3, 3, 3, 16, 16, 16, 42, 16, 16, 1, 1, 60, 60, 160, 21, 5, 5, 3, 42, 42, 126, 16, 16, 1, 1, 1, 1] 603
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 631
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052026 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NN(CO)C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 8, 5, 12, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [70, 32, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 127, 160, 160, 160, 160, 201, 201, 201, 201, 201, 201, 160, 160, 32, 32, 1, 70, 127, 127, 160, 201, 201, 603, 201, 201, 160, 160, 160, 160] 603
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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])
total number of confs: 1289
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052026 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NN(CO)C=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 8, 5, 12, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [73, 73, 73, 128, 137, 201, 201, 201, 201, 201, 21, 16, 10, 9, 1, 9, 1, 1, 1, 1, 8, 1, 1, 16, 16, 128, 128, 201, 73, 21, 21, 10, 8, 8, 24, 1, 1, 16, 16, 16, 16] 603
rigid atoms, others: [35, 36, 14, 16, 17, 18, 19, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40])
total number of confs: 660
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052026 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052026
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052026/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052026
Building REAL300025052027
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052027'
/scratch/stefan/7786831/working/building/REAL300025052027 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052027

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052027/0 /scratch/stefan/7786831/working/building/REAL300025052027 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 932)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/932
`/scratch/stefan/7786831/working/3D/932' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3OC=NC3=CC=C2)CC1)

`REAL300025052027.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052027.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052027/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052027 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3OC=NC3=CC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 25, 87, 102, 189, 189, 189, 189, 189, 6, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 87, 87, 189, 25, 6, 6, 3, 9, 9, 9, 9, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
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: REAL300025052027 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3OC=NC3=CC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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: [74, 33, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 142, 189, 189, 189, 189, 201, 201, 201, 201, 201, 201, 201, 201, 189, 189, 33, 33, 1, 74, 142, 142, 189, 201, 201, 201, 201, 189, 189, 189, 189] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 721
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052027 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3OC=NC3=CC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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: [57, 57, 57, 142, 153, 201, 201, 201, 201, 201, 16, 9, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 142, 142, 201, 57, 16, 16, 6, 1, 1, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 645
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052027 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052027
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052027/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052027
Building REAL300025052028
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052028'
/scratch/stefan/7786831/working/building/REAL300025052028 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052028

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052028/0 /scratch/stefan/7786831/working/building/REAL300025052028 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 933)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/933
`/scratch/stefan/7786831/working/3D/933' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052028.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052028.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052028/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052028 none C#CCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 197, 144, 144, 144, 144, 119, 70, 70, 29, 70, 13, 1, 1, 1, 1, 1, 1, 1, 144, 144, 201, 201, 201, 197, 197, 144, 119, 119, 70, 29, 29, 1, 144, 144, 144, 144] 201
rigid atoms, others: [33, 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, 34, 35, 36, 37])
total number of confs: 841
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052028 none C#CCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 16, 10, 2, 2, 2, 1, 1, 1, 6, 10, 10, 10, 35, 57, 144, 144, 144, 144, 144, 1, 1, 16, 16, 16, 10, 10, 2, 6, 6, 10, 35, 35, 144, 1, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 20, 21] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 365
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052028 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052028
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052028/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052028
Building REAL300025052029
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052029'
/scratch/stefan/7786831/working/building/REAL300025052029 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052029

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052029/0 /scratch/stefan/7786831/working/building/REAL300025052029 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 934)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/934
`/scratch/stefan/7786831/working/3D/934' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CN=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1Cl)

`REAL300025052029.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052029.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052029/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052029 none CC1=CN=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 28, 28, 28, 95, 119, 201, 201, 201, 201, 201, 1, 1, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 28, 95, 95, 201, 1, 1, 1, 1, 4] 201
rigid atoms, others: [37, 38, 7, 8, 9, 39, 40, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 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, 41])
total number of confs: 543
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052029 none CC1=CN=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 12, 40, 40, 40, 108, 130, 201, 201, 201, 201, 201, 4, 4, 1, 1, 1, 2, 2, 2, 1, 4, 12, 12, 40, 108, 108, 201, 4, 4, 4, 4, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 23, 24, 25, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 577
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052029 none CC1=CN=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 129, 58, 58, 29, 58, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 129, 129, 58, 29, 29, 1, 201, 201, 201, 201, 201] 201
rigid atoms, others: [36, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41])
total number of confs: 752
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052029 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052029
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052029/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052029
Building REAL300025052030
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052030'
/scratch/stefan/7786831/working/building/REAL300025052030 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052030

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052030/0 /scratch/stefan/7786831/working/building/REAL300025052030 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 935)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/935
`/scratch/stefan/7786831/working/3D/935' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1CO)

`REAL300025052030.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052030.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052030/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052030 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1CO NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 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]
1  hydrogens need rotated
579  conformations in input
total number of sets (complete confs): 579
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 6, 15, 15, 15, 50, 65, 124, 124, 124, 124, 124, 1, 1, 5, 5, 5, 13, 5, 5, 5, 5, 5, 2, 6, 6, 15, 50, 50, 124, 1, 1, 1, 1, 5, 13, 13, 39] 579
rigid atoms, others: [39, 8, 9, 42, 7, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 43, 44, 45, 46])
total number of confs: 377
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: REAL300025052030 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1CO NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 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]
1  hydrogens need rotated
579  conformations in input
total number of sets (complete confs): 579
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 31, 31, 31, 84, 114, 193, 193, 193, 193, 193, 5, 5, 1, 1, 1, 3, 2, 2, 2, 1, 1, 5, 13, 13, 31, 84, 84, 193, 5, 5, 5, 5, 1, 3, 3, 9] 579
rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 23, 24, 25, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46])
total number of confs: 525
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052030 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1CO NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 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]
1  hydrogens need rotated
579  conformations in input
total number of sets (complete confs): 579
using faster count positions algorithm for large data
unique positions, atoms: [193, 193, 193, 193, 124, 124, 124, 124, 97, 61, 61, 27, 61, 12, 1, 1, 1, 1, 1, 1, 1, 124, 124, 193, 193, 193, 193, 193, 193, 193, 193, 193, 124, 97, 97, 61, 27, 27, 1, 124, 124, 124, 124, 193, 193, 193, 579] 579
rigid atoms, others: [38, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 1188
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052030 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052030
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052030/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052030
Building REAL300025052031
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052031'
/scratch/stefan/7786831/working/building/REAL300025052031 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052031

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052031/0 /scratch/stefan/7786831/working/building/REAL300025052031 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 936)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/936
`/scratch/stefan/7786831/working/3D/936' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC([O-])=CC(=O)O2)CC1)

`REAL300025052031.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052031.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052031/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052031 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC([O-])=CC(=O)O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 12, 1, 1, 11, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 17, 58, 93, 150, 150, 150, 150, 150, 6, 1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 1, 1, 58, 58, 150, 17, 6, 6, 3, 12, 12, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34])
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: REAL300025052031 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC([O-])=CC(=O)O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 12, 1, 1, 11, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 5, 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: [80, 34, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 133, 150, 150, 150, 150, 201, 201, 201, 201, 201, 201, 201, 150, 150, 34, 34, 1, 80, 133, 133, 150, 201, 201, 150, 150, 150, 150] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 673
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052031 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC([O-])=CC(=O)O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 12, 1, 1, 11, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [44, 44, 44, 107, 154, 201, 201, 201, 201, 201, 21, 12, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 107, 107, 201, 44, 21, 21, 7, 1, 1, 12, 12, 12, 12] 201
rigid atoms, others: [33, 34, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38])
total number of confs: 615
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052031 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052031
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052031/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052031
Building REAL300025052032
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052032'
/scratch/stefan/7786831/working/building/REAL300025052032 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052032

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052032/0 /scratch/stefan/7786831/working/building/REAL300025052032 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 937)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/937
`/scratch/stefan/7786831/working/3D/937' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=CC(F)=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1N)

`REAL300025052032.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052032.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052032/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052032 none NC1=CC(F)=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1N NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 6, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 6, 6, 2, 2, 2, 1, 1, 1, 7, 26, 26, 26, 79, 88, 185, 185, 185, 185, 185, 1, 1, 6, 6, 6, 6, 6, 6, 2, 7, 7, 26, 79, 79, 185, 1, 1, 1, 1, 6, 6, 6] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 40, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43])
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: REAL300025052032 none NC1=CC(F)=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1N NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 6, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 19, 58, 58, 58, 135, 144, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 2, 2, 1, 6, 19, 19, 58, 135, 135, 201, 6, 6, 6, 6, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 42, 43, 24, 25, 26, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 638
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052032 none NC1=CC(F)=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1N NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 6, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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
201  conformations 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, 185, 185, 185, 185, 109, 43, 43, 27, 43, 13, 1, 1, 1, 1, 1, 1, 1, 185, 185, 201, 201, 201, 201, 201, 201, 185, 109, 109, 43, 27, 27, 1, 185, 185, 185, 185, 201, 201, 201] 201
rigid atoms, others: [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, 34, 35, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 694
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052032 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052032
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052032/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052032
Building REAL300025052033
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052033'
/scratch/stefan/7786831/working/building/REAL300025052033 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052033

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052033/0 /scratch/stefan/7786831/working/building/REAL300025052033 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 938)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/938
`/scratch/stefan/7786831/working/3D/938' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(F)C=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1N)

`REAL300025052033.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052033.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052033/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052033 none CC1=C(F)C=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1N NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.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, 15, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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: [8, 8, 4, 8, 8, 8, 2, 2, 2, 1, 1, 1, 7, 23, 23, 23, 47, 58, 118, 118, 118, 118, 118, 1, 1, 8, 8, 8, 8, 8, 8, 8, 2, 7, 7, 23, 47, 47, 118, 1, 1, 1, 1, 8, 8] 201
rigid atoms, others: [39, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44])
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: REAL300025052033 none CC1=C(F)C=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1N NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.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, 15, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 29, 63, 63, 63, 109, 123, 201, 201, 201, 201, 201, 8, 8, 1, 1, 2, 2, 2, 1, 1, 8, 29, 29, 63, 109, 109, 201, 8, 8, 8, 8, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 25, 26, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 596
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052033 none CC1=C(F)C=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1N NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.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, 15, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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, 118, 118, 118, 118, 76, 41, 41, 25, 41, 13, 1, 1, 1, 1, 1, 1, 1, 118, 118, 201, 201, 201, 201, 201, 201, 201, 118, 76, 76, 41, 25, 25, 1, 118, 118, 118, 118, 201, 201] 201
rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44])
total number of confs: 569
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052033 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052033
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052033/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052033
Building REAL300025052034
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052034'
/scratch/stefan/7786831/working/building/REAL300025052034 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052034

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052034/0 /scratch/stefan/7786831/working/building/REAL300025052034 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 939)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/939
`/scratch/stefan/7786831/working/3D/939' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=CS1)

`REAL300025052034.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052034.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052034/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052034 none COC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 4, 4, 2, 2, 2, 1, 1, 1, 7, 19, 19, 19, 78, 103, 186, 186, 186, 186, 186, 1, 1, 4, 4, 4, 11, 11, 11, 2, 7, 7, 19, 78, 78, 186, 1, 1, 1, 1, 4, 4] 201
rigid atoms, others: [35, 36, 37, 6, 7, 8, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40])
total number of confs: 497
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052034 none COC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 1, 1, 1, 4, 4, 4, 4, 13, 26, 26, 26, 92, 124, 201, 201, 201, 201, 201, 4, 4, 1, 1, 1, 6, 6, 6, 4, 13, 13, 26, 92, 92, 201, 4, 4, 4, 4, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 39, 40, 22, 23, 24] set([0, 5, 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, 36, 37, 38])
total number of confs: 564
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052034 none COC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 186, 186, 186, 186, 133, 69, 69, 31, 69, 13, 1, 1, 1, 1, 1, 1, 1, 186, 186, 201, 201, 201, 201, 201, 201, 186, 133, 133, 69, 31, 31, 1, 186, 186, 186, 186, 201, 201] 201
rigid atoms, others: [34, 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, 35, 36, 37, 38, 39, 40])
total number of confs: 740
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052034 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052034
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052034/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052034
Building REAL300025052035
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052035'
/scratch/stefan/7786831/working/building/REAL300025052035 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052035

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052035/0 /scratch/stefan/7786831/working/building/REAL300025052035 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 940)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/940
`/scratch/stefan/7786831/working/3D/940' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C(O)CC2CCCCC2)CC1)

`REAL300025052035.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052035.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052035/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052035 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C(O)CC2CCCCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 18, 34, 35, 66, 66, 66, 66, 66, 5, 1, 1, 1, 3, 3, 3, 18, 18, 49, 65, 65, 65, 65, 65, 1, 1, 34, 34, 66, 18, 5, 5, 3, 18, 54, 49, 49, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1] 603
rigid atoms, others: [11, 12, 13, 49, 50, 51, 52, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 492
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: REAL300025052035 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C(O)CC2CCCCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [33, 20, 13, 1, 1, 1, 1, 1, 1, 1, 33, 33, 56, 66, 66, 66, 66, 120, 120, 199, 201, 201, 201, 201, 201, 66, 66, 20, 20, 1, 33, 56, 56, 66, 120, 360, 199, 199, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 66, 66, 66, 66] 603
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 1247
number of broken/clashed sets: 100
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052035 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C(O)CC2CCCCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [157, 157, 157, 193, 194, 201, 201, 201, 201, 201, 80, 65, 50, 50, 13, 50, 5, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 193, 193, 201, 157, 80, 80, 50, 13, 39, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65] 603
rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 49, 50, 51, 52])
total number of confs: 782
number of broken/clashed sets: 100
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052035 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052035
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052035/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052035
Building REAL300025052036
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052036'
/scratch/stefan/7786831/working/building/REAL300025052036 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025052036

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052036/0 /scratch/stefan/7786831/working/building/REAL300025052036 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 941)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/941
`/scratch/stefan/7786831/working/3D/941' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1O)

`REAL300025052036.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052036.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052036/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052036 none N#CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1O NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 12, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 5, 21, 21, 21, 62, 75, 127, 127, 127, 127, 127, 1, 1, 5, 5, 5, 5, 5, 2, 5, 5, 21, 62, 62, 127, 1, 1, 1, 1, 5, 10] 402
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41])
total number of confs: 359
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052036 none N#CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1O NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 12, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 65, 65, 65, 138, 156, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 1, 1, 5, 14, 14, 65, 138, 138, 201, 5, 5, 5, 5, 1, 2] 402
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 40, 24, 25, 26, 27, 28] set([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, 41])
total number of confs: 655
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052036 none N#CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1O NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 12, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
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, 106, 67, 67, 27, 67, 13, 1, 1, 1, 1, 1, 1, 1, 127, 127, 201, 201, 201, 201, 201, 127, 106, 106, 67, 27, 27, 1, 127, 127, 127, 127, 201, 402] 402
rigid atoms, others: [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, 33, 34, 36, 37, 38, 39, 40, 41])
total number of confs: 983
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052036 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025052036/1 /scratch/stefan/7786831/working/building/REAL300025052036 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 942)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/942
`/scratch/stefan/7786831/working/3D/942' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1[O-])

`REAL300025052036.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025052036.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052036/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052036 none N#CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1[O-] NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 12, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 2, 2, 1, 1, 1, 7, 25, 25, 25, 70, 100, 147, 147, 147, 147, 147, 1, 1, 3, 3, 3, 3, 3, 2, 7, 7, 25, 70, 70, 147, 1, 1, 1, 1, 3] 201
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40])
total number of confs: 407
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052036 none N#CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1[O-] NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 12, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 12, 37, 37, 37, 96, 139, 201, 201, 201, 201, 201, 3, 3, 1, 1, 1, 1, 1, 3, 12, 12, 37, 96, 96, 201, 3, 3, 3, 3, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 40, 24, 25, 26, 27, 28] set([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])
total number of confs: 557
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052036 none N#CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1[O-] NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 12, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 147, 147, 147, 147, 129, 78, 78, 36, 78, 13, 1, 1, 1, 1, 1, 1, 1, 147, 147, 201, 201, 201, 201, 201, 147, 129, 129, 78, 36, 36, 1, 147, 147, 147, 147, 201] 201
rigid atoms, others: [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, 33, 34, 36, 37, 38, 39, 40])
total number of confs: 671
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052036 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052036
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025052036/1.*
0: /scratch/stefan/7786831/working/building/REAL300025052036/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052036
Building REAL300025052037
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052037'
/scratch/stefan/7786831/working/building/REAL300025052037 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052037

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052037/0 /scratch/stefan/7786831/working/building/REAL300025052037 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 943)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/943
`/scratch/stefan/7786831/working/3D/943' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3CCCC(C3)C2)CC1)

`REAL300025052037.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052037.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052037/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052037 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3CCCC(C3)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 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: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 51, 61, 118, 118, 118, 118, 118, 5, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 51, 51, 118, 16, 5, 5, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 49, 50, 51, 52, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 326
number of broken/clashed sets: 201
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052037 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3CCCC(C3)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 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: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 28, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 109, 118, 118, 118, 118, 201, 201, 201, 201, 201, 201, 201, 201, 118, 118, 28, 28, 1, 61, 109, 109, 118, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 118, 118, 118, 118] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 724
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052037 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3CCCC(C3)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 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: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 61, 61, 140, 149, 201, 201, 201, 201, 201, 20, 14, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 140, 140, 201, 61, 20, 20, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14] 201
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 49, 50, 51, 52])
total number of confs: 665
number of broken/clashed sets: 201
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052037 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052037
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052037/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052037
Building REAL300025052038
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052038'
/scratch/stefan/7786831/working/building/REAL300025052038 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052038

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052038/0 /scratch/stefan/7786831/working/building/REAL300025052038 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 944)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/944
`/scratch/stefan/7786831/working/3D/944' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=C(F)C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052038.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052038.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052038/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052038 none N#CC1=C(F)C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 7, 21, 21, 21, 61, 83, 175, 175, 175, 175, 175, 1, 1, 9, 9, 9, 2, 7, 7, 21, 61, 61, 175, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
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: REAL300025052038 none N#CC1=C(F)C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 27, 49, 49, 49, 110, 138, 201, 201, 201, 201, 201, 9, 9, 1, 1, 1, 9, 27, 27, 49, 110, 110, 201, 9, 9, 9, 9] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 607
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052038 none N#CC1=C(F)C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 175, 175, 175, 175, 144, 72, 72, 30, 72, 13, 1, 1, 1, 1, 1, 1, 1, 175, 175, 201, 201, 201, 175, 144, 144, 72, 30, 30, 1, 175, 175, 175, 175] 201
rigid atoms, others: [36, 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, 37, 38, 39, 40])
total number of confs: 705
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052038 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052038
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052038/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052038
Building REAL300025052039
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052039'
/scratch/stefan/7786831/working/building/REAL300025052039 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025052039

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052039/0 /scratch/stefan/7786831/working/building/REAL300025052039 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 945)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/945
`/scratch/stefan/7786831/working/3D/945' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(Cl)=NC=C2[O-])CC1)

`REAL300025052039.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052039.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052039/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052039 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(Cl)=NC=C2[O-])CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 16, 8, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [22, 22, 22, 72, 112, 193, 193, 193, 193, 193, 6, 1, 1, 1, 3, 3, 3, 5, 5, 5, 3, 5, 5, 5, 1, 1, 72, 72, 193, 22, 6, 6, 3, 5, 5, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 499
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052039 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(Cl)=NC=C2[O-])CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 16, 8, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [95, 34, 13, 1, 1, 1, 1, 1, 1, 1, 95, 95, 168, 193, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 193, 193, 34, 34, 1, 95, 168, 168, 201, 201, 201, 193, 193, 193, 193] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 772
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052039 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(Cl)=NC=C2[O-])CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 16, 8, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [30, 30, 30, 83, 128, 201, 201, 201, 201, 201, 11, 5, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 83, 83, 201, 30, 11, 11, 3, 1, 1, 5, 5, 5, 5] 201
rigid atoms, others: [33, 34, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38])
total number of confs: 537
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052039 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025052039/1 /scratch/stefan/7786831/working/building/REAL300025052039 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 946)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/946
`/scratch/stefan/7786831/working/3D/946' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(Cl)=NC=C2O)CC1)

`REAL300025052039.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025052039.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052039/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052039 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(Cl)=NC=C2O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 16, 8, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
162  conformations in input
total number of sets (complete confs): 162
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 52, 58, 73, 73, 73, 73, 73, 5, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 1, 1, 52, 52, 73, 22, 5, 5, 3, 6, 6, 12, 1, 1, 1, 1] 162
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 256
number of broken/clashed sets: 38
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052039 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(Cl)=NC=C2O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 16, 8, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
162  conformations in input
total number of sets (complete confs): 162
using faster count positions algorithm for large data
unique positions, atoms: [43, 23, 12, 1, 1, 1, 1, 1, 1, 1, 43, 43, 63, 73, 73, 73, 73, 81, 81, 81, 81, 81, 81, 81, 73, 73, 23, 23, 1, 43, 63, 63, 73, 81, 81, 162, 73, 73, 73, 73] 162
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 441
number of broken/clashed sets: 38
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052039 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(Cl)=NC=C2O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 16, 8, 1, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
162  conformations in input
total number of sets (complete confs): 162
using faster count positions algorithm for large data
unique positions, atoms: [33, 33, 33, 65, 69, 81, 81, 81, 81, 81, 9, 6, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 65, 65, 81, 33, 9, 9, 4, 1, 1, 2, 6, 6, 6, 6] 162
rigid atoms, others: [33, 34, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39])
total number of confs: 282
number of broken/clashed sets: 38
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052039 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052039
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025052039/1.*
0: /scratch/stefan/7786831/working/building/REAL300025052039/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052039
Building REAL300025052040
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052040'
/scratch/stefan/7786831/working/building/REAL300025052040 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052040

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052040/0 /scratch/stefan/7786831/working/building/REAL300025052040 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 947)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/947
`/scratch/stefan/7786831/working/3D/947' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C(C)C)

`REAL300025052040.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052040.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052040/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052040 none CC(=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 157, 157, 157, 157, 134, 72, 72, 28, 72, 13, 1, 1, 1, 1, 1, 1, 1, 157, 157, 201, 201, 201, 201, 201, 201, 201, 157, 134, 134, 72, 28, 28, 1, 157, 157, 157, 157, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [34, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 775
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052040 none CC(=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 2, 2, 2, 1, 1, 1, 6, 10, 10, 10, 35, 62, 157, 157, 157, 157, 157, 1, 1, 9, 12, 12, 9, 9, 9, 9, 2, 6, 6, 10, 35, 35, 157, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12] 201
rigid atoms, others: [35, 36, 5, 6, 7, 19, 20, 38, 37] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 358
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052040 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052040
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052040/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052040
Building REAL300025052041
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052041'
/scratch/stefan/7786831/working/building/REAL300025052041 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052041

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052041/0 /scratch/stefan/7786831/working/building/REAL300025052041 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 948)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/948
`/scratch/stefan/7786831/working/3D/948' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025052041.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052041.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052041/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052041 none COC1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [7, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 4, 17, 17, 17, 40, 48, 77, 77, 77, 77, 77, 1, 1, 5, 7, 7, 7, 5, 5, 2, 4, 4, 17, 40, 40, 77, 1, 1, 1, 1, 5] 95
rigid atoms, others: [38, 39, 40, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42])
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: REAL300025052041 none COC1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 31, 31, 31, 58, 66, 95, 95, 95, 95, 95, 5, 5, 1, 3, 3, 3, 1, 1, 5, 10, 10, 31, 58, 58, 95, 5, 5, 5, 5, 1] 95
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 42, 25, 29, 30] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 292
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052041 none COC1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [95, 95, 95, 95, 95, 95, 77, 77, 77, 77, 66, 46, 46, 25, 46, 12, 1, 1, 1, 1, 1, 1, 1, 77, 77, 95, 95, 95, 95, 95, 95, 77, 66, 66, 46, 25, 25, 1, 77, 77, 77, 77, 95] 95
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 324
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052041 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052041
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052041/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052041
Building REAL300025052042
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052042'
/scratch/stefan/7786831/working/building/REAL300025052042 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052042

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052042/0 /scratch/stefan/7786831/working/building/REAL300025052042 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 949)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/949
`/scratch/stefan/7786831/working/3D/949' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2C[C@@H]3[C@H](C2)C3(F)F)CC1)

`REAL300025052042.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052042.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052042/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052042 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2C[C@@H]3[C@H](C2)C3(F)F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 7, 5, 5, 15, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 20, 63, 74, 147, 147, 147, 147, 147, 5, 1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 63, 63, 147, 20, 5, 5, 3, 12, 12, 12, 12, 12, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
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: REAL300025052042 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2C[C@@H]3[C@H](C2)C3(F)F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 7, 5, 5, 15, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [56, 28, 13, 1, 1, 1, 1, 1, 1, 1, 56, 56, 116, 147, 147, 147, 147, 201, 201, 201, 201, 201, 201, 201, 201, 201, 147, 147, 28, 28, 1, 56, 116, 116, 147, 201, 201, 201, 201, 201, 147, 147, 147, 147] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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])
total number of confs: 762
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052042 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2C[C@@H]3[C@H](C2)C3(F)F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 7, 5, 5, 15, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [69, 69, 69, 138, 153, 201, 201, 201, 201, 201, 21, 12, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 138, 138, 201, 69, 21, 21, 7, 1, 1, 1, 1, 1, 12, 12, 12, 12] 201
rigid atoms, others: [35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43])
total number of confs: 668
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052042 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052042
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052042/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052042
Building REAL300025052043
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052043'
/scratch/stefan/7786831/working/building/REAL300025052043 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052043

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052043/0 /scratch/stefan/7786831/working/building/REAL300025052043 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 950)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/950
`/scratch/stefan/7786831/working/3D/950' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC(O)(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CO1)

`REAL300025052043.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052043.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052043/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052043 none CC1(C)CC(O)(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 12, 12, 9, 12, 2, 2, 2, 1, 1, 1, 7, 20, 20, 20, 62, 90, 175, 175, 175, 175, 175, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 36, 9, 9, 2, 7, 7, 20, 62, 62, 175, 1, 1, 1, 1, 12, 12] 603
rigid atoms, others: [9, 10, 11, 45, 46, 47, 48, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50])
total number of confs: 493
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: REAL300025052043 none CC1(C)CC(O)(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 26, 45, 45, 45, 96, 126, 201, 201, 201, 201, 201, 12, 12, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 6, 5, 5, 12, 26, 26, 45, 96, 96, 201, 12, 12, 12, 12, 1, 1] 603
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 34, 49, 50, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 616
number of broken/clashed sets: 73
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052043 none CC1(C)CC(O)(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 175, 175, 175, 175, 141, 71, 71, 27, 71, 13, 1, 1, 1, 1, 1, 1, 1, 175, 175, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 603, 201, 201, 175, 141, 141, 71, 27, 27, 1, 175, 175, 175, 175, 201, 201] 603
rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50])
total number of confs: 1397
number of broken/clashed sets: 73
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052043 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052043
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052043/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052043
Building REAL300025052044
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052044'
/scratch/stefan/7786831/working/building/REAL300025052044 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052044

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052044/0 /scratch/stefan/7786831/working/building/REAL300025052044 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 951)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/951
`/scratch/stefan/7786831/working/3D/951' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2CC[C@H]3C[C@@H]2CO3)CC1)

`REAL300025052044.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052044.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052044/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052044 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2CC[C@H]3C[C@@H]2CO3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 7, 5, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 25, 84, 101, 172, 172, 172, 172, 172, 5, 1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 84, 84, 172, 25, 5, 5, 3, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1] 201
rigid atoms, others: [47, 44, 11, 12, 13, 46, 45, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 477
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052044 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2CC[C@H]3C[C@@H]2CO3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 7, 5, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 12, 1, 1, 1, 1, 1, 1, 1, 74, 74, 133, 172, 172, 172, 172, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 172, 172, 32, 32, 1, 74, 133, 133, 172, 201, 201, 201, 201, 201, 201, 201, 201, 172, 172, 172, 172] 201
rigid atoms, others: [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, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 750
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052044 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2CC[C@H]3C[C@@H]2CO3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 7, 5, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 147, 163, 201, 201, 201, 201, 201, 19, 12, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 147, 147, 201, 64, 19, 19, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 14, 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, 15, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45, 46, 47])
total number of confs: 666
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052044 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052044
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052044/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052044
Building REAL300025052045
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052045'
/scratch/stefan/7786831/working/building/REAL300025052045 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052045

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052045/0 /scratch/stefan/7786831/working/building/REAL300025052045 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 952)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/952
`/scratch/stefan/7786831/working/3D/952' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1)

`REAL300025052045.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052045.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052045/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052045 none COC1(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 21, 10, 2, 2, 2, 1, 1, 1, 4, 7, 7, 7, 24, 45, 128, 128, 128, 128, 128, 1, 1, 21, 21, 26, 26, 26, 10, 10, 2, 4, 4, 7, 24, 24, 128, 1, 1, 1, 1, 21, 21, 21, 21] 201
rigid atoms, others: [36, 37, 6, 7, 8, 39, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 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, 40, 41, 42, 43])
total number of confs: 317
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052045 none COC1(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 7, 21, 21, 21, 21, 32, 48, 48, 48, 101, 139, 201, 201, 201, 201, 201, 21, 21, 1, 1, 4, 4, 4, 7, 7, 21, 32, 32, 48, 101, 101, 201, 21, 21, 21, 21, 1, 1, 1, 1] 201
rigid atoms, others: [1, 2, 3, 40, 41, 42, 43, 22, 23] set([0, 4, 5, 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])
total number of confs: 625
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052045 none COC1(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 192, 128, 128, 128, 128, 105, 71, 71, 31, 71, 13, 1, 1, 1, 1, 1, 1, 1, 128, 128, 201, 201, 201, 201, 201, 192, 192, 128, 105, 105, 71, 31, 31, 1, 128, 128, 128, 128, 201, 201, 201, 201] 201
rigid atoms, others: [35, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 866
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052045 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052045
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052045/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052045
Building REAL300025052046
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052046'
/scratch/stefan/7786831/working/building/REAL300025052046 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052046

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052046/0 /scratch/stefan/7786831/working/building/REAL300025052046 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 953)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/953
`/scratch/stefan/7786831/working/3D/953' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CNC3=CC=CC=C32)CC1)

`REAL300025052046.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052046.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052046/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052046 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CNC3=CC=CC=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 25, 86, 94, 172, 172, 172, 172, 172, 6, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 86, 86, 172, 25, 6, 6, 3, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 469
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052046 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CNC3=CC=CC=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 33, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 151, 172, 172, 172, 172, 201, 201, 201, 201, 201, 201, 201, 201, 172, 172, 33, 33, 1, 74, 151, 151, 172, 201, 201, 201, 201, 201, 201, 201, 201, 172, 172, 172, 172] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45])
total number of confs: 768
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052046 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CNC3=CC=CC=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [54, 54, 54, 131, 138, 201, 201, 201, 201, 201, 19, 11, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 131, 131, 201, 54, 19, 19, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44, 45])
total number of confs: 627
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052046 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052046
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052046/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052046
Building REAL300025052047
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052047'
/scratch/stefan/7786831/working/building/REAL300025052047 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052047

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052047/0 /scratch/stefan/7786831/working/building/REAL300025052047 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 954)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/954
`/scratch/stefan/7786831/working/3D/954' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC2=C(C=C(C(=O)NC3(CNC(=O)CSC4=NNC(=O)[N-]4)CC3)N2)O1)

`REAL300025052047.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052047.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052047/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052047 none CC1=CC2=C(C=C(C(=O)NC3(CNC(=O)CSC4=NNC(=O)[N-]4)CC3)N2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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: [6, 6, 6, 6, 6, 6, 2, 2, 2, 1, 1, 1, 7, 32, 32, 32, 95, 117, 201, 201, 201, 201, 201, 1, 1, 6, 6, 6, 6, 6, 6, 6, 2, 7, 7, 32, 95, 95, 201, 1, 1, 1, 1, 6] 201
rigid atoms, others: [39, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43])
total number of confs: 541
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052047 none CC1=CC2=C(C=C(C(=O)NC3(CNC(=O)CSC4=NNC(=O)[N-]4)CC3)N2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 17, 49, 49, 49, 116, 134, 201, 201, 201, 201, 201, 6, 6, 1, 1, 2, 2, 2, 1, 1, 6, 17, 17, 49, 116, 116, 201, 6, 6, 6, 6, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 43, 25, 26, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 584
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052047 none CC1=CC2=C(C=C(C(=O)NC3(CNC(=O)CSC4=NNC(=O)[N-]4)CC3)N2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 201, 201, 201, 201, 201, 201, 201, 147, 60, 60, 28, 60, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 147, 147, 60, 28, 28, 1, 201, 201, 201, 201, 201] 201
rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43])
total number of confs: 754
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052047 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052047
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052047/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052047
Building REAL300025052048
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052048'
/scratch/stefan/7786831/working/building/REAL300025052048 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052048

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052048/0 /scratch/stefan/7786831/working/building/REAL300025052048 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 955)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/955
`/scratch/stefan/7786831/working/3D/955' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNC1=C(N)C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052048.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052048.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052048/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052048 none CNC1=C(N)C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 1, 1, 1, 7, 22, 22, 22, 82, 122, 199, 199, 199, 199, 199, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 7, 7, 22, 82, 82, 199, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 11, 12, 13, 46, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 512
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052048 none CNC1=C(N)C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 6, 6, 6, 6, 16, 38, 38, 38, 100, 136, 201, 201, 201, 201, 201, 6, 6, 3, 3, 3, 3, 2, 2, 1, 1, 1, 6, 16, 16, 38, 100, 100, 201, 6, 6, 6, 6] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 8, 9, 7, 34, 35] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 567
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052048 none CNC1=C(N)C=CC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 199, 199, 199, 199, 151, 83, 83, 28, 83, 13, 1, 1, 1, 1, 1, 1, 1, 199, 199, 201, 201, 201, 201, 201, 201, 201, 201, 201, 199, 151, 151, 83, 28, 28, 1, 199, 199, 199, 199] 201
rigid atoms, others: [42, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46])
total number of confs: 751
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052048 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052048
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052048/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052048
Building REAL300025052049
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052049'
/scratch/stefan/7786831/working/building/REAL300025052049 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052049

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052049/0 /scratch/stefan/7786831/working/building/REAL300025052049 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 956)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/956
`/scratch/stefan/7786831/working/3D/956' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1)

`REAL300025052049.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052049.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052049/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052049 none CN1N=CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 12, 12, 10, 2, 2, 2, 1, 1, 1, 6, 15, 15, 15, 54, 79, 160, 160, 160, 160, 160, 1, 1, 12, 12, 12, 12, 12, 10, 10, 2, 6, 6, 15, 54, 54, 160, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 8, 9, 10, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
total number of confs: 408
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052049 none CN1N=CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 12, 12, 12, 12, 25, 38, 38, 38, 90, 122, 201, 201, 201, 201, 201, 12, 12, 1, 2, 2, 2, 1, 4, 4, 12, 25, 25, 38, 90, 90, 201, 12, 12, 12, 12] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 28] set([6, 7, 8, 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: 573
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052049 none CN1N=CC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 160, 160, 160, 160, 126, 69, 69, 30, 69, 13, 1, 1, 1, 1, 1, 1, 1, 160, 160, 201, 201, 201, 201, 201, 201, 201, 160, 126, 126, 69, 30, 30, 1, 160, 160, 160, 160] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41])
total number of confs: 834
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052049 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052049
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052049/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052049
Building REAL300025052050
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052050'
/scratch/stefan/7786831/working/building/REAL300025052050 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052050

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052050/0 /scratch/stefan/7786831/working/building/REAL300025052050 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 957)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/957
`/scratch/stefan/7786831/working/3D/957' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2(C3CCCCO3)CC2)CC1)

`REAL300025052050.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052050.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052050/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052050 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2(C3CCCCO3)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 68, 80, 146, 146, 146, 146, 146, 6, 1, 1, 1, 3, 3, 3, 7, 14, 14, 14, 14, 14, 7, 7, 1, 1, 68, 68, 146, 20, 6, 6, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 47, 48, 49, 50, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025052050 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2(C3CCCCO3)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 27, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 125, 146, 146, 146, 146, 173, 201, 201, 201, 201, 201, 173, 173, 146, 146, 27, 27, 1, 69, 125, 125, 146, 201, 201, 201, 201, 201, 201, 201, 201, 201, 173, 173, 173, 173, 146, 146, 146, 146] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46, 47, 48, 49, 50])
total number of confs: 756
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052050 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2(C3CCCCO3)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 125, 143, 201, 201, 201, 201, 201, 19, 14, 10, 10, 6, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 14, 125, 125, 201, 59, 19, 19, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 14] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 609
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052050 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2(C3CCCCO3)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 38, 38, 96, 111, 173, 173, 173, 173, 173, 11, 7, 5, 5, 1, 5, 1, 1, 6, 6, 6, 6, 6, 1, 1, 7, 7, 96, 96, 173, 38, 11, 11, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [43, 44, 45, 14, 16, 17, 46, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50])
total number of confs: 510
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052050 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052050
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052050/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052050
Building REAL300025052051
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052051'
/scratch/stefan/7786831/working/building/REAL300025052051 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025052051

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052051/0 /scratch/stefan/7786831/working/building/REAL300025052051 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 958)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/958
`/scratch/stefan/7786831/working/3D/958' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2N=CC(=O)[N-]C2=O)CC1)

`REAL300025052051.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052051.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052051/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052051 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2N=CC(=O)[N-]C2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 11, 8, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 31, 50, 115, 115, 115, 115, 115, 6, 1, 1, 1, 3, 3, 3, 10, 14, 14, 14, 14, 14, 14, 14, 1, 1, 31, 31, 115, 16, 6, 6, 3, 10, 10, 14, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 285
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052051 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2N=CC(=O)[N-]C2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 11, 8, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 29, 13, 1, 1, 1, 1, 1, 1, 1, 56, 56, 105, 115, 115, 115, 115, 192, 201, 201, 201, 201, 201, 201, 201, 115, 115, 29, 29, 1, 56, 105, 105, 115, 192, 192, 201, 115, 115, 115, 115] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 856
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052051 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2N=CC(=O)[N-]C2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 11, 8, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 56, 56, 91, 126, 201, 201, 201, 201, 201, 28, 14, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 91, 91, 201, 56, 28, 28, 9, 3, 3, 1, 14, 14, 14, 14] 201
rigid atoms, others: [36, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 582
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052051 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025052051/1 /scratch/stefan/7786831/working/building/REAL300025052051 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 959)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/959
`/scratch/stefan/7786831/working/3D/959' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2N=CC(=O)NC2=O)CC1)

`REAL300025052051.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025052051.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052051/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052051 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2N=CC(=O)NC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 11, 8, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
130  conformations in input
total number of sets (complete confs): 130
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 32, 41, 74, 74, 74, 74, 74, 4, 1, 1, 1, 3, 3, 3, 18, 29, 29, 29, 29, 29, 29, 29, 1, 1, 32, 32, 74, 13, 4, 4, 3, 18, 18, 29, 29, 1, 1, 1, 1] 130
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 262
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052051 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2N=CC(=O)NC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 11, 8, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
130  conformations in input
total number of sets (complete confs): 130
using faster count positions algorithm for large data
unique positions, atoms: [45, 22, 13, 1, 1, 1, 1, 1, 1, 1, 45, 45, 69, 74, 74, 74, 74, 116, 130, 130, 130, 130, 130, 130, 130, 74, 74, 22, 22, 1, 45, 69, 69, 74, 116, 116, 130, 130, 74, 74, 74, 74] 130
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 503
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052051 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CN2N=CC(=O)NC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 11, 8, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
130  conformations in input
total number of sets (complete confs): 130
using faster count positions algorithm for large data
unique positions, atoms: [74, 74, 74, 105, 111, 130, 130, 130, 130, 130, 37, 29, 22, 21, 3, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 105, 105, 130, 74, 37, 37, 22, 3, 3, 1, 1, 29, 29, 29, 29] 130
rigid atoms, others: [36, 37, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41])
total number of confs: 444
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052051 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052051
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025052051/1.*
0: /scratch/stefan/7786831/working/building/REAL300025052051/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052051
Building REAL300025052052
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052052'
/scratch/stefan/7786831/working/building/REAL300025052052 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052052

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052052/0 /scratch/stefan/7786831/working/building/REAL300025052052 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 960)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/960
`/scratch/stefan/7786831/working/3D/960' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CC2(F)F)CC1)

`REAL300025052052.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052052.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052052/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052052 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CC2(F)F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 28, 37, 97, 97, 97, 97, 97, 5, 1, 1, 1, 3, 3, 3, 19, 48, 48, 48, 48, 1, 1, 28, 28, 97, 12, 5, 5, 3, 19, 19, 48, 48, 48, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 358
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052052 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CC2(F)F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [62, 31, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 91, 97, 97, 97, 97, 185, 201, 201, 201, 201, 97, 97, 31, 31, 1, 62, 91, 91, 97, 185, 185, 201, 201, 201, 97, 97, 97, 97] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 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: 823
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052052 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CC2(F)F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [99, 99, 99, 136, 164, 201, 201, 201, 201, 201, 60, 48, 32, 32, 6, 32, 1, 1, 1, 1, 1, 1, 48, 48, 136, 136, 201, 99, 60, 60, 32, 6, 6, 1, 1, 1, 48, 48, 48, 48] 201
rigid atoms, others: [33, 34, 35, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39])
total number of confs: 660
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052052 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052052
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052052/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052052
Building REAL300025052053
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052053'
/scratch/stefan/7786831/working/building/REAL300025052053 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052053

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052053/0 /scratch/stefan/7786831/working/building/REAL300025052053 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 961)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/961
`/scratch/stefan/7786831/working/3D/961' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CN=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025052053.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052053.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052053/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052053 none COC1=CN=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 27, 27, 27, 69, 88, 195, 196, 196, 196, 196, 1, 1, 4, 5, 5, 5, 4, 2, 7, 7, 27, 69, 69, 196, 1, 1, 1, 1, 4] 201
rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41])
total number of confs: 472
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052053 none COC1=CN=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 14, 45, 45, 45, 100, 118, 201, 201, 201, 201, 201, 4, 4, 1, 3, 3, 3, 1, 4, 14, 14, 45, 100, 100, 201, 4, 4, 4, 4, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 41, 25, 29] set([0, 8, 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])
total number of confs: 554
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052053 none COC1=CN=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 196, 196, 196, 196, 134, 63, 63, 29, 63, 13, 1, 1, 1, 1, 1, 1, 1, 196, 196, 201, 201, 201, 201, 201, 196, 134, 134, 63, 29, 29, 1, 196, 196, 196, 196, 201] 201
rigid atoms, others: [36, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41])
total number of confs: 724
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052053 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052053
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052053/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052053
Building REAL300025052054
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052054'
/scratch/stefan/7786831/working/building/REAL300025052054 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052054

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052054/0 /scratch/stefan/7786831/working/building/REAL300025052054 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 962)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/962
`/scratch/stefan/7786831/working/3D/962' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CN1C=CN=C1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052054.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052054.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052054/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052054 none CC(CN1C=CN=C1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 2, 6, 11, 21, 21, 21, 21, 2, 2, 1, 1, 1, 5, 9, 9, 9, 26, 42, 106, 106, 106, 106, 106, 1, 1, 6, 6, 6, 6, 11, 11, 21, 21, 21, 2, 5, 5, 9, 26, 26, 106, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 287
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052054 none CC(CN1C=CN=C1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 11, 21, 21, 21, 21, 30, 45, 45, 45, 92, 125, 201, 201, 201, 201, 201, 21, 21, 11, 11, 11, 11, 5, 5, 1, 1, 1, 21, 30, 30, 45, 92, 92, 201, 21, 21, 21, 21] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 603
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052054 none CC(CN1C=CN=C1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [143, 106, 143, 152, 201, 201, 201, 201, 106, 106, 106, 89, 53, 53, 26, 53, 12, 1, 1, 1, 1, 1, 1, 1, 106, 106, 143, 143, 143, 143, 152, 152, 201, 201, 201, 106, 89, 89, 53, 26, 26, 1, 106, 106, 106, 106] 201
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 754
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052054 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052054
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052054/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052054
Building REAL300025052055
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052055'
/scratch/stefan/7786831/working/building/REAL300025052055 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052055

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052055/0 /scratch/stefan/7786831/working/building/REAL300025052055 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 963)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/963
`/scratch/stefan/7786831/working/3D/963' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(=O)NC=N2)CC1)

`REAL300025052055.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052055.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052055/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052055 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(=O)NC=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 30, 106, 116, 198, 198, 198, 198, 198, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 1, 1, 106, 106, 198, 30, 6, 6, 3, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
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: REAL300025052055 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(=O)NC=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [74, 32, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 151, 198, 198, 198, 198, 201, 201, 201, 201, 201, 201, 198, 198, 32, 32, 1, 74, 151, 151, 198, 201, 201, 201, 198, 198, 198, 198] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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])
total number of confs: 746
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052055 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(=O)NC=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [49, 49, 49, 124, 131, 201, 201, 201, 201, 201, 13, 7, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 124, 124, 201, 49, 13, 13, 4, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38])
total number of confs: 596
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052055 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052055
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052055/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052055
Building REAL300025052056
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052056'
/scratch/stefan/7786831/working/building/REAL300025052056 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052056

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052056/0 /scratch/stefan/7786831/working/building/REAL300025052056 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 964)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/964
`/scratch/stefan/7786831/working/3D/964' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCN1C=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1)

`REAL300025052056.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052056.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052056/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052056 none CCCN1C=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 5, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 7, 15, 15, 15, 53, 64, 125, 125, 125, 125, 125, 1, 1, 2, 7, 7, 7, 7, 7, 5, 5, 2, 2, 2, 7, 7, 15, 53, 53, 125, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 352
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052056 none CCCN1C=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 15, 15, 15, 53, 64, 125, 125, 125, 125, 125, 2, 2, 1, 7, 7, 7, 7, 7, 5, 5, 1, 1, 2, 7, 7, 15, 53, 53, 125, 2, 2, 2, 2] 201
rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 25] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 352
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052056 none CCCN1C=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 125, 125, 125, 125, 125, 125, 125, 125, 87, 48, 48, 28, 48, 13, 1, 1, 1, 1, 1, 1, 1, 125, 125, 125, 201, 201, 201, 201, 201, 201, 201, 125, 125, 125, 87, 87, 48, 28, 28, 1, 125, 125, 125, 125] 201
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 948
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052056 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052056
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052056/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052056
Building REAL300025052057
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052057'
/scratch/stefan/7786831/working/building/REAL300025052057 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052057

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052057/0 /scratch/stefan/7786831/working/building/REAL300025052057 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 965)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/965
`/scratch/stefan/7786831/working/3D/965' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=C1F)

`REAL300025052057.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052057.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052057/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052057 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 7, 29, 29, 29, 91, 111, 201, 201, 201, 201, 201, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 29, 91, 91, 201, 1, 1, 1, 1] 201
rigid atoms, others: [38, 7, 8, 9, 39, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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])
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: REAL300025052057 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 13, 40, 40, 40, 108, 128, 201, 201, 201, 201, 201, 3, 3, 1, 1, 1, 2, 2, 2, 1, 1, 3, 13, 13, 40, 108, 108, 201, 3, 3, 3, 3] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 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])
total number of confs: 594
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052057 none CC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)N=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 141, 65, 65, 29, 65, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 141, 141, 65, 29, 29, 1, 201, 201, 201, 201] 201
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41])
total number of confs: 740
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052057 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052057
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052057/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052057
Building REAL300025052058
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052058'
/scratch/stefan/7786831/working/building/REAL300025052058 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052058

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052058/0 /scratch/stefan/7786831/working/building/REAL300025052058 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 966)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/966
`/scratch/stefan/7786831/working/3D/966' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(CO)C=N2)CC1)

`REAL300025052058.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052058.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052058/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052058 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(CO)C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 12, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 20, 49, 52, 144, 144, 144, 144, 144, 5, 1, 1, 1, 3, 3, 3, 19, 19, 19, 19, 63, 19, 19, 1, 1, 49, 49, 144, 20, 5, 5, 3, 19, 19, 63, 63, 189, 19, 1, 1, 1, 1] 603
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
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: REAL300025052058 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(CO)C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 12, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [63, 31, 13, 1, 1, 1, 1, 1, 1, 1, 63, 63, 120, 144, 144, 144, 144, 201, 201, 201, 201, 201, 201, 201, 144, 144, 31, 31, 1, 63, 120, 120, 144, 201, 201, 201, 201, 603, 201, 144, 144, 144, 144] 603
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 1251
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052058 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(CO)C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 12, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [75, 75, 75, 126, 128, 201, 201, 201, 201, 201, 27, 19, 12, 11, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 19, 19, 126, 126, 201, 75, 27, 27, 12, 1, 1, 8, 8, 24, 1, 19, 19, 19, 19] 603
rigid atoms, others: [33, 34, 38, 14, 16, 17, 18, 19, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 659
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052058 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052058
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052058/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052058
Building REAL300025052059
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052059'
/scratch/stefan/7786831/working/building/REAL300025052059 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025052059

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052059/0 /scratch/stefan/7786831/working/building/REAL300025052059 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 967)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/967
`/scratch/stefan/7786831/working/3D/967' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@H+]1CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1)

`REAL300025052059.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052059.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052059/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052059 none C[N@H+]1CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 6, 6, 6, 4, 2, 2, 2, 1, 1, 1, 3, 5, 5, 5, 10, 11, 12, 12, 12, 12, 12, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 2, 3, 3, 5, 10, 10, 12, 1, 1, 1, 1, 6, 6, 6, 6] 13
rigid atoms, others: [43, 9, 10, 11, 44, 45, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49])
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: REAL300025052059 none C[N@H+]1CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 6, 6, 7, 8, 8, 8, 12, 13, 13, 13, 13, 13, 13, 6, 6, 1, 1, 2, 2, 2, 1, 1, 1, 5, 5, 6, 7, 7, 8, 12, 12, 13, 6, 6, 6, 6, 1, 1, 1, 1] 13
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 46, 47, 48, 49, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 59
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052059 none C[N@H+]1CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [13, 13, 13, 13, 13, 13, 12, 12, 12, 12, 12, 12, 12, 11, 12, 7, 1, 1, 1, 1, 1, 1, 1, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12, 12, 12, 11, 11, 1, 12, 12, 12, 12, 13, 13, 13, 13] 13
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 36
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052059 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025052059/1 /scratch/stefan/7786831/working/building/REAL300025052059 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 968)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/968
`/scratch/stefan/7786831/working/3D/968' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@@H+]1CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1)

`REAL300025052059.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025052059.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052059/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052059 none C[N@@H+]1CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 6, 6, 6, 4, 2, 2, 2, 1, 1, 1, 3, 5, 5, 5, 10, 11, 12, 12, 12, 12, 12, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 2, 3, 3, 5, 10, 10, 12, 1, 1, 1, 1, 6, 6, 6, 6] 13
rigid atoms, others: [43, 9, 10, 11, 44, 45, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49])
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: REAL300025052059 none C[N@@H+]1CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 6, 6, 7, 8, 8, 8, 12, 13, 13, 13, 13, 13, 13, 6, 6, 1, 1, 2, 2, 2, 1, 1, 1, 5, 5, 6, 7, 7, 8, 12, 12, 13, 6, 6, 6, 6, 1, 1, 1, 1] 13
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 46, 47, 48, 49, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 59
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052059 none C[N@@H+]1CC=C(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [13, 13, 13, 13, 13, 13, 12, 12, 12, 12, 12, 12, 12, 11, 12, 7, 1, 1, 1, 1, 1, 1, 1, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12, 12, 12, 11, 11, 1, 12, 12, 12, 12, 13, 13, 13, 13] 13
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 36
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052059 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052059
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025052059/1.*
0: /scratch/stefan/7786831/working/building/REAL300025052059/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052059
Building REAL300025052060
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052060'
/scratch/stefan/7786831/working/building/REAL300025052060 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052060

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052060/0 /scratch/stefan/7786831/working/building/REAL300025052060 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 969)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/969
`/scratch/stefan/7786831/working/3D/969' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@H](C)[C@H](O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052060.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052060.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052060/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052060 none CC[C@H](C)[C@H](O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 199, 201, 201, 170, 199, 199, 170, 170, 170, 121, 59, 59, 28, 59, 13, 1, 1, 1, 1, 1, 1, 1, 170, 170, 201, 201, 201, 201, 201, 201, 201, 201, 597, 170, 121, 121, 59, 28, 28, 1, 170, 170, 170, 170] 603
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 1422
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052060 none CC[C@H](C)[C@H](O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 4, 7, 7, 2, 4, 4, 2, 2, 1, 1, 1, 7, 14, 14, 14, 52, 69, 170, 170, 170, 170, 170, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 12, 2, 7, 7, 14, 52, 52, 170, 1, 1, 1, 1] 603
rigid atoms, others: [43, 44, 10, 11, 12, 45, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 417
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052060 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052060
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052060/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052060
Building REAL300025052061
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052061'
/scratch/stefan/7786831/working/building/REAL300025052061 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052061

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052061/0 /scratch/stefan/7786831/working/building/REAL300025052061 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 970)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/970
`/scratch/stefan/7786831/working/3D/970' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=CC1=CC=C(F)N=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052061.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052061.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052061/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052061 none O=C(C=CC1=CC=C(F)N=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 1, 15, 8, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 10, 10, 22, 22, 22, 22, 22, 22, 1, 1, 1, 4, 8, 8, 8, 23, 38, 108, 108, 108, 108, 108, 1, 1, 10, 10, 22, 22, 22, 2, 4, 4, 8, 23, 23, 108, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 257
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052061 none O=C(C=CC1=CC=C(F)N=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 1, 15, 8, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 40, 57, 57, 57, 107, 131, 201, 201, 201, 201, 201, 22, 22, 5, 5, 1, 1, 1, 22, 40, 40, 57, 107, 107, 201, 22, 22, 22, 22] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 639
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052061 none O=C(C=CC1=CC=C(F)N=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 1, 15, 8, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [108, 108, 108, 174, 174, 201, 201, 201, 201, 201, 201, 108, 87, 48, 48, 26, 48, 12, 1, 1, 1, 1, 1, 1, 1, 108, 108, 174, 174, 201, 201, 201, 108, 87, 87, 48, 26, 26, 1, 108, 108, 108, 108] 201
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42])
total number of confs: 708
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052061 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052061
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052061/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052061
Building REAL300025052062
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052062'
/scratch/stefan/7786831/working/building/REAL300025052062 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052062

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052062/0 /scratch/stefan/7786831/working/building/REAL300025052062 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 971)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/971
`/scratch/stefan/7786831/working/3D/971' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C(C)C)

`REAL300025052062.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052062.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052062/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052062 none CC(C)CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 180, 167, 167, 167, 167, 129, 64, 64, 29, 64, 13, 1, 1, 1, 1, 1, 1, 1, 167, 167, 180, 200, 200, 201, 201, 201, 201, 201, 201, 201, 201, 201, 180, 167, 129, 129, 64, 29, 29, 1, 167, 167, 167, 167, 200, 200, 200, 200, 200, 200, 200] 201
rigid atoms, others: [42, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 975
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: REAL300025052062 none CC(C)CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 2, 2, 1, 1, 1, 7, 16, 16, 16, 54, 81, 167, 167, 167, 167, 167, 1, 1, 3, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 2, 7, 7, 16, 54, 54, 167, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4] 201
rigid atoms, others: [7, 8, 9, 43, 44, 45, 46, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 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, 41, 42, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 417
number of broken/clashed sets: 115
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052062 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052062
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052062/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052062
Building REAL300025052063
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052063'
/scratch/stefan/7786831/working/building/REAL300025052063 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052063

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052063/0 /scratch/stefan/7786831/working/building/REAL300025052063 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 972)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/972
`/scratch/stefan/7786831/working/3D/972' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC(O)C(F)(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052063.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052063.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052063/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052063 none O=C(CCC(O)C(F)(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 12, 5, 15, 15, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [96, 96, 96, 185, 191, 201, 201, 201, 201, 201, 96, 80, 51, 51, 25, 51, 12, 1, 1, 1, 1, 1, 1, 1, 96, 96, 185, 185, 195, 195, 201, 603, 96, 80, 80, 51, 25, 25, 1, 96, 96, 96, 96] 603
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42])
total number of confs: 1518
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052063 none O=C(CCC(O)C(F)(F)F)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 12, 5, 15, 15, 15, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 10, 12, 23, 23, 23, 23, 23, 1, 1, 1, 4, 7, 7, 7, 22, 35, 96, 96, 96, 96, 96, 1, 1, 10, 10, 14, 14, 23, 69, 2, 4, 4, 7, 22, 22, 96, 1, 1, 1, 1] 603
rigid atoms, others: [39, 40, 41, 10, 11, 12, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 368
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052063 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052063
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052063/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052063
Building REAL300025052064
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052064'
/scratch/stefan/7786831/working/building/REAL300025052064 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052064

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052064/0 /scratch/stefan/7786831/working/building/REAL300025052064 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 973)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/973
`/scratch/stefan/7786831/working/3D/973' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=NC(C=CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025052064.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052064.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052064/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052064 none CN1C=NC(C=CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 8, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 9, 7, 7, 2, 2, 2, 1, 1, 1, 6, 15, 15, 15, 58, 96, 191, 191, 191, 191, 191, 1, 1, 9, 9, 9, 9, 9, 7, 7, 2, 6, 6, 15, 58, 58, 191, 1, 1, 1, 1, 9] 201
rigid atoms, others: [39, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43])
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: REAL300025052064 none CN1C=NC(C=CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 8, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 8, 9, 9, 9, 19, 34, 34, 34, 98, 134, 201, 201, 201, 201, 201, 9, 9, 1, 2, 2, 2, 1, 3, 4, 9, 19, 19, 34, 98, 98, 201, 9, 9, 9, 9, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 25, 29] set([6, 7, 8, 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])
total number of confs: 571
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052064 none CN1C=NC(C=CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 8, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 191, 191, 191, 191, 151, 86, 86, 32, 86, 13, 1, 1, 1, 1, 1, 1, 1, 191, 191, 201, 201, 201, 201, 201, 201, 201, 191, 151, 151, 86, 32, 32, 1, 191, 191, 191, 191, 201] 201
rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43])
total number of confs: 765
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052064 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052064
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052064/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052064
Building REAL300025052065
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052065'
/scratch/stefan/7786831/working/building/REAL300025052065 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025052065

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052065/0 /scratch/stefan/7786831/working/building/REAL300025052065 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 974)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/974
`/scratch/stefan/7786831/working/3D/974' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=NN=C(C3CC3)N2)CC1)

`REAL300025052065.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052065.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052065/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052065 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=NN=C(C3CC3)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 5, 5, 5, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 16, 16, 35, 39, 59, 59, 59, 59, 59, 5, 1, 1, 1, 3, 3, 3, 17, 22, 22, 22, 22, 65, 65, 22, 1, 1, 35, 35, 59, 16, 5, 5, 3, 17, 17, 65, 65, 65, 65, 65, 22, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 352
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: REAL300025052065 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=NN=C(C3CC3)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 5, 5, 5, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 18, 13, 1, 1, 1, 1, 1, 1, 1, 29, 29, 51, 59, 59, 59, 59, 121, 130, 130, 130, 130, 201, 201, 130, 59, 59, 18, 18, 1, 29, 51, 51, 59, 121, 121, 201, 201, 201, 201, 201, 130, 59, 59, 59, 59] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45])
total number of confs: 774
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052065 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=NN=C(C3CC3)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 5, 5, 5, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [141, 141, 141, 196, 200, 201, 201, 201, 201, 201, 79, 65, 62, 62, 25, 62, 12, 12, 12, 12, 1, 1, 1, 1, 12, 65, 65, 196, 196, 201, 141, 79, 79, 62, 25, 25, 1, 1, 1, 1, 1, 12, 65, 65, 65, 65] 201
rigid atoms, others: [36, 37, 38, 39, 40, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45])
total number of confs: 797
number of broken/clashed sets: 2
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052065 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=NN=C(C3CC3)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 5, 5, 5, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [64, 64, 64, 100, 104, 130, 130, 130, 130, 130, 28, 22, 19, 19, 4, 19, 1, 1, 1, 1, 1, 1, 12, 12, 1, 22, 22, 100, 100, 130, 64, 28, 28, 19, 4, 4, 12, 12, 12, 12, 12, 1, 22, 22, 22, 22] 201
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 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, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 496
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052065 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025052065/1 /scratch/stefan/7786831/working/building/REAL300025052065 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 975)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/975
`/scratch/stefan/7786831/working/3D/975' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=NNC(C3CC3)=N2)CC1)

`REAL300025052065.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025052065.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052065/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052065 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=NNC(C3CC3)=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 5, 5, 5, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 19, 19, 36, 36, 36, 36, 36, 4, 1, 1, 1, 3, 3, 3, 14, 39, 39, 39, 39, 84, 84, 39, 1, 1, 19, 19, 36, 10, 4, 4, 3, 14, 14, 39, 84, 84, 84, 84, 84, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 331
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052065 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=NNC(C3CC3)=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 5, 5, 5, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 10, 10, 1, 1, 1, 1, 1, 1, 1, 14, 14, 29, 36, 36, 36, 36, 70, 142, 142, 142, 142, 201, 201, 142, 36, 36, 10, 10, 1, 14, 29, 29, 36, 70, 70, 142, 201, 201, 201, 201, 201, 36, 36, 36, 36] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45])
total number of confs: 621
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052065 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=NNC(C3CC3)=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 5, 5, 5, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 151, 151, 199, 199, 201, 201, 201, 201, 201, 95, 84, 76, 76, 30, 76, 10, 10, 10, 10, 1, 1, 1, 1, 10, 84, 84, 199, 199, 201, 151, 95, 95, 76, 30, 30, 10, 1, 1, 1, 1, 1, 84, 84, 84, 84] 201
rigid atoms, others: [37, 38, 39, 40, 41, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45])
total number of confs: 793
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052065 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=NNC(C3CC3)=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 5, 5, 5, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [84, 84, 84, 120, 120, 142, 142, 142, 142, 142, 47, 39, 31, 31, 8, 31, 1, 1, 1, 1, 1, 1, 10, 10, 1, 39, 39, 120, 120, 142, 84, 47, 47, 31, 8, 8, 1, 10, 10, 10, 10, 10, 39, 39, 39, 39] 201
rigid atoms, others: [36, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 564
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052065 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052065
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025052065/1.*
0: /scratch/stefan/7786831/working/building/REAL300025052065/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052065
Building REAL300025052066
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052066'
/scratch/stefan/7786831/working/building/REAL300025052066 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052066

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052066/0 /scratch/stefan/7786831/working/building/REAL300025052066 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 976)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/976
`/scratch/stefan/7786831/working/3D/976' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052066.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052066.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052066/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052066 none CC1(C)CC1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 27, 27, 15, 10, 2, 2, 2, 1, 1, 1, 4, 6, 6, 6, 21, 32, 89, 89, 89, 89, 89, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 17, 17, 10, 10, 2, 4, 4, 6, 21, 21, 89, 1, 1, 1, 1] 201
rigid atoms, others: [9, 10, 11, 45, 46, 47, 48, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 294
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052066 none CC1(C)CC1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 7, 27, 27, 27, 27, 54, 75, 75, 75, 122, 140, 201, 201, 201, 201, 201, 27, 27, 2, 2, 2, 2, 2, 2, 1, 1, 1, 4, 4, 7, 7, 27, 54, 54, 75, 122, 122, 201, 27, 27, 27, 27] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 33, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 712
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052066 none CC1(C)CC1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 193, 188, 89, 89, 89, 89, 76, 47, 47, 25, 47, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 188, 188, 89, 76, 76, 47, 25, 25, 1, 89, 89, 89, 89] 201
rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48])
total number of confs: 890
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052066 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052066
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052066/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052066
Building REAL300025052067
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052067'
/scratch/stefan/7786831/working/building/REAL300025052067 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052067

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052067/0 /scratch/stefan/7786831/working/building/REAL300025052067 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 977)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/977
`/scratch/stefan/7786831/working/3D/977' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2CCCO2)CC1)

`REAL300025052067.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052067.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052067/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052067 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2CCCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 14, 38, 42, 95, 95, 95, 95, 95, 5, 1, 1, 1, 3, 3, 3, 23, 23, 23, 23, 23, 55, 55, 55, 55, 1, 1, 38, 38, 95, 14, 5, 5, 3, 23, 23, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1] 201
rigid atoms, others: [47, 12, 11, 44, 13, 46, 45, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 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: REAL300025052067 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2CCCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [49, 30, 13, 1, 1, 1, 1, 1, 1, 1, 49, 49, 84, 95, 95, 95, 95, 177, 177, 177, 177, 177, 201, 201, 201, 201, 95, 95, 30, 30, 1, 49, 84, 84, 95, 177, 177, 201, 201, 201, 201, 201, 201, 201, 95, 95, 95, 95] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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, 46, 47])
total number of confs: 707
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052067 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2CCCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 125, 125, 180, 181, 201, 201, 201, 201, 201, 66, 55, 40, 40, 6, 40, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 55, 55, 180, 180, 201, 125, 66, 66, 40, 6, 6, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55] 201
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 19, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47])
total number of confs: 747
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052067 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2C[C@H]2C2CCCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 134, 138, 177, 177, 177, 177, 177, 31, 23, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 23, 23, 134, 134, 177, 78, 31, 31, 13, 1, 1, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 23] 201
rigid atoms, others: [35, 36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 629
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052067 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052067
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052067/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052067
Building REAL300025052068
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052068'
/scratch/stefan/7786831/working/building/REAL300025052068 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052068

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052068/0 /scratch/stefan/7786831/working/building/REAL300025052068 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 978)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/978
`/scratch/stefan/7786831/working/3D/978' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCS2(=O)=O)CC1)

`REAL300025052068.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052068.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052068/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052068 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCS2(=O)=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 26, 26, 83, 97, 186, 186, 186, 186, 186, 6, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 1, 1, 83, 83, 186, 26, 6, 6, 3, 11, 11, 11, 11, 11, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 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: REAL300025052068 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCS2(=O)=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [85, 36, 13, 1, 1, 1, 1, 1, 1, 1, 85, 85, 154, 186, 186, 186, 186, 201, 201, 201, 201, 201, 186, 186, 36, 36, 1, 85, 154, 154, 186, 201, 201, 201, 201, 201, 186, 186, 186, 186] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 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: 758
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052068 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCS2(=O)=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [59, 59, 59, 127, 140, 201, 201, 201, 201, 201, 21, 11, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 11, 11, 127, 127, 201, 59, 21, 21, 9, 1, 1, 1, 1, 1, 11, 11, 11, 11] 201
rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39])
total number of confs: 611
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052068 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052068
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052068/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052068
Building REAL300025052069
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052069'
/scratch/stefan/7786831/working/building/REAL300025052069 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025052069

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052069/0 /scratch/stefan/7786831/working/building/REAL300025052069 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 979)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/979
`/scratch/stefan/7786831/working/3D/979' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=C3N=CNC3=C2)CC1)

`REAL300025052069.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052069.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052069/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052069 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=C3N=CNC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [29, 29, 29, 93, 102, 191, 191, 191, 191, 191, 7, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 93, 93, 191, 29, 7, 7, 3, 5, 5, 5, 5, 1, 1, 1, 1] 191
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 505
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052069 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=C3N=CNC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [57, 31, 13, 1, 1, 1, 1, 1, 1, 1, 57, 57, 140, 191, 191, 191, 191, 191, 191, 191, 191, 191, 191, 191, 191, 191, 191, 31, 31, 1, 57, 140, 140, 191, 191, 191, 191, 191, 191, 191, 191, 191] 191
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 722
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052069 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=C3N=CNC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [45, 45, 45, 116, 122, 191, 191, 191, 191, 191, 12, 5, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 116, 116, 191, 45, 12, 12, 4, 1, 1, 1, 1, 5, 5, 5, 5] 191
rigid atoms, others: [34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 578
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052069 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025052069/1 /scratch/stefan/7786831/working/building/REAL300025052069 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 980)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/980
`/scratch/stefan/7786831/working/3D/980' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=C3NC=NC3=C2)CC1)

`REAL300025052069.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025052069.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052069/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052069 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=C3NC=NC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 29, 107, 120, 201, 201, 201, 201, 201, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 107, 107, 201, 29, 6, 6, 3, 7, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 559
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052069 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=C3NC=NC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 29, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 150, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 29, 29, 1, 65, 150, 150, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 737
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052069 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NC=C3NC=NC3=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 1, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 118, 128, 201, 201, 201, 201, 201, 12, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 118, 118, 201, 45, 12, 12, 4, 1, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 578
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052069 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052069
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025052069/1.*
0: /scratch/stefan/7786831/working/building/REAL300025052069/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052069
Building REAL300025052070
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052070'
/scratch/stefan/7786831/working/building/REAL300025052070 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052070

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052070/0 /scratch/stefan/7786831/working/building/REAL300025052070 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 981)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/981
`/scratch/stefan/7786831/working/3D/981' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[S+](C)CCC(O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052070.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052070.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052070/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
Warning: Using closest atom type 60 for atom 2
Warning: Using closest atom type 60 for atom 2
('energy: ', 12.0)
('conf: ', 200)
Warning: Using closest atom type 60 for atom 2
Warning: Using closest atom type 60 for atom 2
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052070 none C[S+](C)CCC(O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 182, 201, 182, 156, 125, 156, 125, 125, 125, 102, 69, 69, 30, 69, 13, 1, 1, 1, 1, 1, 1, 1, 125, 125, 201, 201, 201, 201, 201, 201, 182, 182, 182, 182, 156, 468, 125, 102, 102, 69, 30, 30, 1, 125, 125, 125, 125] 603
rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47])
total number of confs: 1361
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052070 none C[S+](C)CCC(O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [25, 12, 25, 11, 4, 2, 4, 2, 2, 1, 1, 1, 3, 6, 6, 6, 23, 47, 125, 125, 125, 125, 125, 1, 1, 25, 25, 25, 25, 25, 25, 12, 12, 11, 11, 4, 12, 2, 3, 3, 6, 23, 23, 125, 1, 1, 1, 1] 603
rigid atoms, others: [9, 10, 11, 44, 45, 46, 47, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 337
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052070 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052070
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052070/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052070
Building REAL300025052071
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052071'
/scratch/stefan/7786831/working/building/REAL300025052071 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052071

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052071/0 /scratch/stefan/7786831/working/building/REAL300025052071 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 982)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/982
`/scratch/stefan/7786831/working/3D/982' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1CCCC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025052071.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052071.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052071/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052071 none N#CC1CCCC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 17, 17, 17, 17, 9, 2, 2, 2, 1, 1, 1, 6, 10, 10, 10, 29, 45, 124, 124, 124, 124, 124, 1, 1, 16, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 2, 6, 6, 10, 29, 29, 124, 1, 1, 1, 1, 17, 17] 201
rigid atoms, others: [44, 10, 11, 12, 45, 46, 47, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49])
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: REAL300025052071 none N#CC1CCCC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 17, 32, 49, 49, 49, 103, 130, 201, 201, 201, 201, 201, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 32, 32, 49, 103, 103, 201, 17, 17, 17, 17, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 33, 49, 48, 26, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 626
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052071 none N#CC1CCCC(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 200, 124, 124, 124, 124, 106, 62, 62, 29, 62, 13, 1, 1, 1, 1, 1, 1, 1, 124, 124, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 124, 106, 106, 62, 29, 29, 1, 124, 124, 124, 124, 201, 201] 201
rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49])
total number of confs: 840
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052071 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052071
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052071/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052071
Building REAL300025052072
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052072'
/scratch/stefan/7786831/working/building/REAL300025052072 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052072

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052072/0 /scratch/stefan/7786831/working/building/REAL300025052072 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 983)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/983
`/scratch/stefan/7786831/working/3D/983' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C(O)CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052072.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052072.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052072/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052072 none CC(C)(C)C(O)CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 184, 106, 106, 106, 106, 93, 54, 54, 26, 54, 13, 1, 1, 1, 1, 1, 1, 1, 106, 106, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 603, 201, 201, 184, 184, 106, 93, 93, 54, 26, 26, 1, 106, 106, 106, 106] 603
rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51])
total number of confs: 1517
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: REAL300025052072 none CC(C)(C)C(O)CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [21, 21, 21, 21, 15, 21, 10, 2, 2, 2, 1, 1, 1, 4, 8, 8, 8, 24, 39, 106, 106, 106, 106, 106, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 63, 16, 16, 10, 10, 2, 4, 4, 8, 24, 24, 106, 1, 1, 1, 1] 603
rigid atoms, others: [10, 11, 12, 48, 49, 50, 51, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 375
number of broken/clashed sets: 57
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052072 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052072
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052072/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052072
Building REAL300025052073
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052073'
/scratch/stefan/7786831/working/building/REAL300025052073 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052073

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052073/0 /scratch/stefan/7786831/working/building/REAL300025052073 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 984)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/984
`/scratch/stefan/7786831/working/3D/984' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=CC1=CC=CC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052073.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052073.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052073/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052073 none O=C(C=CC1=CC=CC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 9, 9, 14, 14, 9, 14, 14, 1, 1, 1, 4, 8, 8, 8, 24, 41, 106, 106, 106, 106, 106, 1, 1, 9, 9, 14, 14, 9, 14, 14, 2, 4, 4, 8, 24, 24, 106, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 10, 11, 12, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 266
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052073 none O=C(C=CC1=CC=CC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 3, 3, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 33, 52, 52, 52, 112, 142, 201, 201, 201, 201, 201, 14, 14, 3, 3, 1, 1, 1, 1, 1, 14, 33, 33, 52, 112, 112, 201, 14, 14, 14, 14] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 644
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052073 none O=C(C=CC1=CC=CC=C1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [106, 106, 106, 201, 201, 201, 201, 201, 201, 201, 106, 89, 53, 53, 25, 53, 12, 1, 1, 1, 1, 1, 1, 1, 106, 106, 201, 201, 201, 201, 201, 201, 201, 106, 89, 89, 53, 25, 25, 1, 106, 106, 106, 106] 201
rigid atoms, others: [39, 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, 40, 41, 42, 43])
total number of confs: 717
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052073 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052073
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052073/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052073
Building REAL300025052074
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052074'
/scratch/stefan/7786831/working/building/REAL300025052074 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052074

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052074/0 /scratch/stefan/7786831/working/building/REAL300025052074 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 985)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/985
`/scratch/stefan/7786831/working/3D/985' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NOC(C(F)F)=C2)CC1)

`REAL300025052074.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052074.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052074/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052074 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NOC(C(F)F)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'F', 'F', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 15, 15, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 19, 21, 45, 45, 45, 45, 45, 4, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 37, 37, 13, 1, 1, 19, 19, 45, 9, 4, 4, 3, 37, 13, 1, 1, 1, 1] 70
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 235
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052074 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NOC(C(F)F)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'F', 'F', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 15, 15, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [31, 17, 11, 1, 1, 1, 1, 1, 1, 1, 31, 31, 44, 45, 45, 45, 45, 70, 70, 70, 70, 70, 70, 70, 45, 45, 17, 17, 1, 31, 44, 44, 45, 70, 70, 45, 45, 45, 45] 70
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 214
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052074 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=NOC(C(F)F)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'F', 'F', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 15, 15, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [28, 28, 28, 43, 45, 70, 70, 70, 70, 70, 16, 13, 8, 8, 1, 8, 1, 1, 1, 1, 1, 10, 10, 1, 13, 13, 43, 43, 70, 28, 16, 16, 8, 10, 1, 13, 13, 13, 13] 70
rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 251
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052074 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052074
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052074/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052074
Building REAL300025052075
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052075'
/scratch/stefan/7786831/working/building/REAL300025052075 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052075

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052075/0 /scratch/stefan/7786831/working/building/REAL300025052075 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 986)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/986
`/scratch/stefan/7786831/working/3D/986' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=CC=C(Cl)Cl)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052075.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052075.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052075/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052075 none O=C(C=CC=C(Cl)Cl)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'Cl', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 1, 16, 16, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [144, 144, 144, 201, 201, 201, 201, 201, 144, 106, 45, 45, 25, 45, 11, 1, 1, 1, 1, 1, 1, 1, 144, 144, 201, 201, 201, 144, 106, 106, 45, 25, 25, 1, 144, 144, 144, 144] 201
rigid atoms, others: [33, 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, 34, 35, 36, 37])
total number of confs: 742
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052075 none O=C(C=CC=C(Cl)Cl)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'Cl', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 1, 16, 16, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 8, 8, 8, 8, 8, 1, 1, 1, 6, 17, 17, 17, 55, 68, 144, 144, 144, 144, 144, 1, 1, 8, 8, 8, 2, 6, 6, 17, 55, 55, 144, 1, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 371
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052075 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052075
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052075/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052075
Building REAL300025052076
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052076'
/scratch/stefan/7786831/working/building/REAL300025052076 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052076

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052076/0 /scratch/stefan/7786831/working/building/REAL300025052076 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 987)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/987
`/scratch/stefan/7786831/working/3D/987' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)(C)C(O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052076.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052076.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052076/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052076 none CCC(C)(C)C(O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 99, 201, 201, 99, 99, 99, 99, 99, 70, 32, 32, 20, 32, 11, 1, 1, 1, 1, 1, 1, 1, 99, 99, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 99, 297, 99, 70, 70, 32, 20, 20, 1, 99, 99, 99, 99] 603
rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48])
total number of confs: 1179
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052076 none CCC(C)(C)C(O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [6, 4, 2, 4, 4, 2, 2, 2, 2, 1, 1, 1, 6, 16, 16, 16, 36, 39, 99, 99, 99, 99, 99, 1, 1, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 4, 2, 6, 2, 6, 6, 16, 36, 36, 99, 1, 1, 1, 1] 603
rigid atoms, others: [9, 10, 11, 45, 46, 47, 48, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 268
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052076 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052076
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052076/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052076
Building REAL300025052077
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052077'
/scratch/stefan/7786831/working/building/REAL300025052077 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052077

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052077/0 /scratch/stefan/7786831/working/building/REAL300025052077 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 988)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/988
`/scratch/stefan/7786831/working/3D/988' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)(C)C(=O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052077.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052077.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052077/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052077 none CCC(C)(C)C(=O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 128, 201, 201, 111, 128, 111, 111, 111, 79, 44, 44, 24, 44, 13, 1, 1, 1, 1, 1, 1, 1, 111, 111, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 111, 79, 79, 44, 24, 24, 1, 111, 111, 111, 111] 201
rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46])
total number of confs: 893
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052077 none CCC(C)(C)C(=O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 13, 5, 13, 13, 2, 5, 2, 2, 1, 1, 1, 7, 21, 21, 21, 49, 57, 111, 111, 111, 111, 111, 1, 1, 15, 15, 15, 15, 15, 13, 13, 13, 13, 13, 13, 2, 7, 7, 21, 49, 49, 111, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 46, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 377
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052077 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052077
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052077/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052077
Building REAL300025052078
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052078'
/scratch/stefan/7786831/working/building/REAL300025052078 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052078

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052078/0 /scratch/stefan/7786831/working/building/REAL300025052078 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 989)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/989
`/scratch/stefan/7786831/working/3D/989' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=NC=C(O)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052078.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052078.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052078/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052078 none NC1=NC=C(O)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 8, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 3, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 9, 9, 2, 2, 2, 1, 1, 1, 7, 21, 21, 21, 57, 66, 143, 143, 143, 143, 143, 1, 1, 9, 9, 9, 18, 9, 2, 7, 7, 21, 57, 57, 143, 1, 1, 1, 1] 402
rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
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: REAL300025052078 none NC1=NC=C(O)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 8, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 3, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 24, 58, 58, 58, 126, 133, 201, 201, 201, 201, 201, 9, 9, 2, 2, 1, 2, 1, 9, 24, 24, 58, 126, 126, 201, 9, 9, 9, 9] 402
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 28, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 633
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052078 none NC1=NC=C(O)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 8, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 3, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 143, 143, 143, 143, 102, 51, 51, 26, 51, 13, 1, 1, 1, 1, 1, 1, 1, 143, 143, 201, 201, 201, 402, 201, 143, 102, 102, 51, 26, 26, 1, 143, 143, 143, 143] 402
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41])
total number of confs: 1039
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052078 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052078
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052078/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052078
Building REAL300025052079
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052079'
/scratch/stefan/7786831/working/building/REAL300025052079 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052079

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052079/0 /scratch/stefan/7786831/working/building/REAL300025052079 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 990)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/990
`/scratch/stefan/7786831/working/3D/990' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1CC2CC2(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025052079.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052079.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052079/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052079 none CC(=O)N1CC2CC2(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 6, 11, 6, 6, 6, 6, 2, 2, 2, 1, 1, 1, 6, 24, 24, 24, 62, 87, 141, 141, 141, 141, 141, 1, 1, 6, 11, 11, 11, 6, 6, 6, 6, 6, 2, 6, 6, 24, 62, 62, 141, 1, 1, 1, 1, 6, 6] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47])
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: REAL300025052079 none CC(=O)N1CC2CC2(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 14, 48, 48, 48, 99, 127, 175, 175, 175, 175, 175, 6, 6, 1, 4, 4, 4, 1, 1, 1, 1, 1, 6, 14, 14, 48, 99, 99, 175, 6, 6, 6, 6, 1, 1] 201
rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 46, 47, 33, 26, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 517
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052079 none CC(=O)N1CC2CC2(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 175, 201, 175, 175, 175, 175, 141, 141, 141, 141, 127, 75, 75, 34, 75, 13, 1, 1, 1, 1, 1, 1, 1, 141, 141, 175, 201, 201, 201, 175, 175, 175, 175, 175, 141, 127, 127, 75, 34, 34, 1, 141, 141, 141, 141, 175, 175] 201
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47])
total number of confs: 688
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052079 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052079
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052079/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052079
Building REAL300025052080
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052080'
/scratch/stefan/7786831/working/building/REAL300025052080 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052080

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052080/0 /scratch/stefan/7786831/working/building/REAL300025052080 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 991)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/991
`/scratch/stefan/7786831/working/3D/991' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCC3(CCC3)O2)CC1)

`REAL300025052080.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052080.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052080/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052080 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCC3(CCC3)O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 14, 36, 39, 85, 85, 85, 85, 85, 5, 1, 1, 1, 3, 3, 3, 21, 43, 43, 43, 43, 43, 43, 43, 1, 1, 36, 36, 85, 14, 5, 5, 3, 21, 21, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 47, 48, 49, 50, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025052080 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCC3(CCC3)O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 27, 13, 1, 1, 1, 1, 1, 1, 1, 38, 38, 70, 85, 85, 85, 85, 185, 201, 201, 201, 201, 201, 201, 201, 85, 85, 27, 27, 1, 38, 70, 70, 85, 185, 185, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 85, 85, 85, 85] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46, 47, 48, 49, 50])
total number of confs: 822
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052080 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2CCC3(CCC3)O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [121, 121, 121, 175, 176, 201, 201, 201, 201, 201, 60, 43, 31, 31, 6, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 175, 175, 201, 121, 60, 60, 31, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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, 47, 48, 49, 50])
total number of confs: 763
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052080 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052080
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052080/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052080
Building REAL300025052081
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052081'
/scratch/stefan/7786831/working/building/REAL300025052081 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052081

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052081/0 /scratch/stefan/7786831/working/building/REAL300025052081 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 992)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/992
`/scratch/stefan/7786831/working/3D/992' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCCCC3=CN2)CC1)

`REAL300025052081.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052081.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052081/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052081 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCCCC3=CN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 17, 47, 53, 78, 78, 78, 78, 78, 5, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 47, 47, 78, 17, 5, 5, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1] 83
rigid atoms, others: [44, 11, 12, 13, 46, 45, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 245
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052081 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCCCC3=CN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [44, 26, 13, 1, 1, 1, 1, 1, 1, 1, 44, 44, 68, 78, 78, 78, 78, 83, 83, 83, 83, 83, 83, 83, 83, 78, 78, 26, 26, 1, 44, 68, 68, 78, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 78, 78, 78, 78] 83
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46, 47])
total number of confs: 305
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052081 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C3CCCCC3=CN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [45, 45, 45, 68, 72, 83, 83, 83, 83, 83, 19, 14, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 68, 68, 83, 45, 19, 19, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14] 83
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 44, 45, 46, 47])
total number of confs: 292
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052081 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052081
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052081/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052081
Building REAL300025052082
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052082'
/scratch/stefan/7786831/working/building/REAL300025052082 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052082

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052082/0 /scratch/stefan/7786831/working/building/REAL300025052082 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 993)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/993
`/scratch/stefan/7786831/working/3D/993' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1)

`REAL300025052082.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052082.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052082/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052082 none NC1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 29, 29, 29, 101, 118, 200, 200, 200, 200, 200, 1, 1, 4, 4, 4, 4, 4, 2, 7, 7, 29, 101, 101, 200, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 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: REAL300025052082 none NC1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 40, 40, 40, 115, 131, 201, 201, 201, 201, 201, 4, 4, 1, 1, 1, 1, 1, 4, 11, 11, 40, 115, 115, 201, 4, 4, 4, 4] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 25, 26, 27, 28] set([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])
total number of confs: 582
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052082 none NC1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 200, 200, 200, 200, 134, 59, 59, 30, 59, 13, 1, 1, 1, 1, 1, 1, 1, 200, 200, 201, 201, 201, 201, 201, 200, 134, 134, 59, 30, 30, 1, 200, 200, 200, 200] 201
rigid atoms, others: [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, 33, 34, 36, 37, 38, 39])
total number of confs: 762
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052082 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052082
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052082/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052082
Building REAL300025052083
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052083'
/scratch/stefan/7786831/working/building/REAL300025052083 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052083

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052083/0 /scratch/stefan/7786831/working/building/REAL300025052083 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 994)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/994
`/scratch/stefan/7786831/working/3D/994' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CC1CC2(C1)CC(C(=O)NC1(CNC(=O)CSC3=NNC(=O)[N-]3)CC1)C2)

`REAL300025052083.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052083.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052083/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052083 none C#CC1CC2(C1)CC(C(=O)NC1(CNC(=O)CSC3=NNC(=O)[N-]3)CC1)C2 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 2, 2, 2, 1, 1, 1, 6, 14, 14, 14, 36, 42, 113, 113, 113, 113, 113, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 6, 6, 14, 36, 36, 113, 1, 1, 1, 1, 8, 8] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48])
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: REAL300025052083 none C#CC1CC2(C1)CC(C(=O)NC1(CNC(=O)CSC3=NNC(=O)[N-]3)CC1)C2 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 26, 51, 51, 51, 105, 116, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 26, 26, 51, 105, 105, 201, 8, 8, 8, 8, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 47, 33, 35, 48, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 614
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052083 none C#CC1CC2(C1)CC(C(=O)NC1(CNC(=O)CSC3=NNC(=O)[N-]3)CC1)C2 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 113, 113, 113, 113, 78, 40, 40, 25, 40, 12, 1, 1, 1, 1, 1, 1, 1, 113, 113, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 113, 78, 78, 40, 25, 25, 1, 113, 113, 113, 113, 201, 201] 201
rigid atoms, others: [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, 40, 41, 43, 44, 45, 46, 47, 48])
total number of confs: 710
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052083 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052083
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052083/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052083
Building REAL300025052084
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052084'
/scratch/stefan/7786831/working/building/REAL300025052084 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052084

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052084/0 /scratch/stefan/7786831/working/building/REAL300025052084 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 995)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/995
`/scratch/stefan/7786831/working/3D/995' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSC1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1)

`REAL300025052084.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052084.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052084/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052084 none CSC1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 19, 19, 19, 73, 100, 197, 197, 197, 197, 197, 1, 1, 4, 10, 10, 10, 4, 4, 2, 7, 7, 19, 73, 73, 197, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 499
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052084 none CSC1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 11, 24, 24, 24, 81, 109, 201, 201, 201, 201, 201, 4, 4, 1, 8, 8, 8, 1, 1, 4, 11, 11, 24, 81, 81, 201, 4, 4, 4, 4] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 25, 29, 30] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 538
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052084 none CSC1=CN=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 197, 197, 197, 197, 134, 63, 63, 30, 63, 13, 1, 1, 1, 1, 1, 1, 1, 197, 197, 201, 201, 201, 201, 201, 201, 197, 134, 134, 63, 30, 30, 1, 197, 197, 197, 197] 201
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41])
total number of confs: 761
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052084 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052084
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052084/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052084
Building REAL300025052085
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052085'
/scratch/stefan/7786831/working/building/REAL300025052085 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052085

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052085/0 /scratch/stefan/7786831/working/building/REAL300025052085 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 996)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/996
`/scratch/stefan/7786831/working/3D/996' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052085.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052085.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052085/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052085 none CC=CC=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 161, 161, 161, 161, 116, 70, 70, 32, 70, 13, 1, 1, 1, 1, 1, 1, 1, 161, 161, 201, 201, 201, 201, 201, 201, 201, 161, 116, 116, 70, 32, 32, 1, 161, 161, 161, 161] 201
rigid atoms, others: [36, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 763
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052085 none CC=CC=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 7, 16, 16, 16, 58, 85, 161, 161, 161, 161, 161, 1, 1, 9, 9, 9, 9, 9, 9, 9, 2, 7, 7, 16, 58, 58, 161, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 7, 8, 9, 39, 40, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 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])
total number of confs: 405
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052085 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052085
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052085/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052085
Building REAL300025052086
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052086'
/scratch/stefan/7786831/working/building/REAL300025052086 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052086

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052086/0 /scratch/stefan/7786831/working/building/REAL300025052086 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 997)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/997
`/scratch/stefan/7786831/working/3D/997' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1)

`REAL300025052086.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052086.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052086/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052086 none COCCN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 29, 16, 3, 3, 3, 2, 2, 2, 1, 1, 1, 4, 8, 8, 8, 18, 18, 74, 74, 74, 74, 74, 1, 1, 3, 3, 61, 61, 61, 29, 29, 16, 16, 3, 2, 4, 4, 8, 18, 18, 74, 1, 1, 1, 1, 3] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46])
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052086 none COCCN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [44, 17, 9, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 12, 12, 12, 26, 26, 90, 90, 90, 90, 90, 3, 3, 1, 1, 44, 44, 44, 17, 17, 9, 9, 1, 3, 6, 6, 12, 26, 26, 90, 3, 3, 3, 3, 1] 201
rigid atoms, others: [34, 3, 4, 5, 6, 7, 46, 25, 26] set([0, 1, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 308
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052086 none COCCN1C=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 179, 90, 90, 90, 74, 74, 74, 74, 58, 45, 45, 29, 45, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 90, 90, 201, 201, 201, 201, 201, 179, 179, 90, 74, 58, 58, 45, 29, 29, 1, 74, 74, 74, 74, 90] 201
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46])
total number of confs: 863
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052086 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052086
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052086/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052086
Building REAL300025052087
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052087'
/scratch/stefan/7786831/working/building/REAL300025052087 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052087

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052087/0 /scratch/stefan/7786831/working/building/REAL300025052087 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 998)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/998
`/scratch/stefan/7786831/working/3D/998' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1[C@@H](C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)[C@@H](O)C(=O)N1C)

`REAL300025052087.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052087.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052087/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052087 none C[C@@H]1[C@@H](C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)[C@@H](O)C(=O)N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', '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, 7, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 12, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 2, 7, 2, 2, 1, 1, 1, 7, 27, 27, 27, 73, 98, 182, 182, 182, 182, 182, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 7, 7, 27, 73, 73, 182, 1, 1, 1, 1, 21, 7, 7, 7] 603
rigid atoms, others: [7, 8, 9, 42, 43, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 44, 45, 46, 47])
total number of confs: 494
number of broken/clashed sets: 61
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052087 none C[C@@H]1[C@@H](C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)[C@@H](O)C(=O)N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', '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, 7, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 12, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 20, 51, 51, 51, 104, 129, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 20, 20, 51, 104, 104, 201, 7, 7, 7, 7, 3, 2, 2, 2] 603
rigid atoms, others: [0, 1, 2, 3, 4, 5, 23, 24, 25, 26, 27, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 602
number of broken/clashed sets: 61
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052087 none C[C@@H]1[C@@H](C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)[C@@H](O)C(=O)N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', '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, 7, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 12, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 182, 201, 182, 182, 182, 144, 78, 78, 32, 78, 13, 1, 1, 1, 1, 1, 1, 1, 182, 182, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 182, 144, 144, 78, 32, 32, 1, 182, 182, 182, 182, 603, 201, 201, 201] 603
rigid atoms, others: [39, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 1353
number of broken/clashed sets: 61
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052087 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052087
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052087/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052087
Building REAL300025052088
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052088'
/scratch/stefan/7786831/working/building/REAL300025052088 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052088

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052088/0 /scratch/stefan/7786831/working/building/REAL300025052088 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 999)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/999
`/scratch/stefan/7786831/working/3D/999' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CN=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052088.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052088.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052088/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052088 none CN1N=CN=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 6, 31, 31, 31, 114, 134, 200, 200, 200, 200, 200, 1, 1, 4, 4, 4, 4, 2, 6, 6, 31, 114, 114, 200, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
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: REAL300025052088 none CN1N=CN=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 12, 47, 47, 47, 131, 148, 201, 201, 201, 201, 201, 4, 4, 2, 2, 2, 1, 4, 12, 12, 47, 131, 131, 201, 4, 4, 4, 4] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 628
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052088 none CN1N=CN=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 200, 200, 200, 200, 166, 64, 64, 26, 64, 13, 1, 1, 1, 1, 1, 1, 1, 200, 200, 201, 201, 201, 201, 200, 166, 166, 64, 26, 26, 1, 200, 200, 200, 200] 201
rigid atoms, others: [34, 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, 35, 36, 37, 38])
total number of confs: 745
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052088 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052088
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052088/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052088
Building REAL300025052089
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052089'
/scratch/stefan/7786831/working/building/REAL300025052089 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052089

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052089/0 /scratch/stefan/7786831/working/building/REAL300025052089 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1000)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1000
`/scratch/stefan/7786831/working/3D/1000' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2CC[C@@H](O)C2)CC1)

`REAL300025052089.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052089.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052089/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052089 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2CC[C@@H](O)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 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]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 18, 58, 73, 144, 144, 144, 144, 144, 5, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 1, 1, 58, 58, 144, 18, 5, 5, 3, 15, 15, 15, 15, 45, 15, 15, 1, 1, 1, 1] 603
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 422
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052089 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2CC[C@@H](O)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 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]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [73, 32, 12, 1, 1, 1, 1, 1, 1, 1, 73, 73, 128, 144, 144, 144, 144, 201, 201, 201, 201, 201, 201, 201, 144, 144, 32, 32, 1, 73, 128, 128, 144, 201, 201, 201, 201, 603, 201, 201, 144, 144, 144, 144] 603
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 1340
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052089 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2CC[C@@H](O)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 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]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [66, 66, 66, 147, 157, 201, 201, 201, 201, 201, 20, 15, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 147, 147, 201, 66, 20, 20, 8, 1, 1, 1, 1, 6, 1, 1, 15, 15, 15, 15] 603
rigid atoms, others: [33, 34, 35, 36, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 40, 41, 42, 43])
total number of confs: 685
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052089 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052089
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052089/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052089
Building REAL300025052090
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052090'
/scratch/stefan/7786831/working/building/REAL300025052090 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052090

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052090/0 /scratch/stefan/7786831/working/building/REAL300025052090 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1001)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1001
`/scratch/stefan/7786831/working/3D/1001' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)C=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052090.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052090.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052090/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052090 none CS(=O)C=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 190, 190, 190, 190, 141, 71, 71, 33, 71, 13, 1, 1, 1, 1, 1, 1, 1, 190, 190, 201, 201, 201, 201, 201, 190, 141, 141, 71, 33, 33, 1, 190, 190, 190, 190] 201
rigid atoms, others: [34, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
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: REAL300025052090 none CS(=O)C=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 7, 15, 7, 2, 2, 2, 1, 1, 1, 6, 15, 15, 15, 57, 85, 190, 190, 190, 190, 190, 1, 1, 15, 15, 15, 7, 7, 2, 6, 6, 15, 57, 57, 190, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 459
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052090 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052090
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052090/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052090
Building REAL300025052091
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052091'
/scratch/stefan/7786831/working/building/REAL300025052091 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052091

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052091/0 /scratch/stefan/7786831/working/building/REAL300025052091 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1002)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1002
`/scratch/stefan/7786831/working/3D/1002' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(C)(C)O1)

`REAL300025052091.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052091.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052091/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052091 none CC1(C)CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(C)(C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 7, 27, 27, 27, 84, 104, 199, 199, 199, 199, 199, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 7, 7, 27, 84, 84, 199, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5] 201
rigid atoms, others: [7, 8, 9, 43, 44, 45, 46, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 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, 41, 42, 47, 48, 49, 50, 51, 52])
total number of confs: 511
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: REAL300025052091 none CC1(C)CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(C)(C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 15, 42, 42, 42, 106, 125, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 5, 15, 15, 42, 106, 106, 201, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 34, 35, 23, 24, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 595
number of broken/clashed sets: 37
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052091 none CC1(C)CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(C)(C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 199, 199, 199, 141, 63, 63, 29, 63, 13, 1, 1, 1, 1, 1, 1, 1, 199, 199, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 199, 141, 141, 63, 29, 29, 1, 199, 199, 199, 199, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [42, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 747
number of broken/clashed sets: 37
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052091 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052091
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052091/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052091
Building REAL300025052092
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052092'
/scratch/stefan/7786831/working/building/REAL300025052092 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052092

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052092/0 /scratch/stefan/7786831/working/building/REAL300025052092 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1003)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1003
`/scratch/stefan/7786831/working/3D/1003' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(Cl)=CN=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052092.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052092.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052092/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052092 none CN1C(Cl)=CN=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'Cl', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 16, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 6, 33, 33, 33, 117, 140, 199, 199, 199, 199, 199, 1, 1, 4, 4, 4, 4, 2, 6, 6, 33, 117, 117, 199, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 570
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052092 none CN1C(Cl)=CN=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'Cl', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 16, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 12, 52, 52, 52, 139, 157, 201, 201, 201, 201, 201, 4, 4, 2, 2, 2, 1, 4, 12, 12, 52, 139, 139, 201, 4, 4, 4, 4] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 630
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052092 none CN1C(Cl)=CN=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'Cl', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 16, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 199, 199, 199, 199, 158, 70, 70, 29, 70, 13, 1, 1, 1, 1, 1, 1, 1, 199, 199, 201, 201, 201, 201, 199, 158, 158, 70, 29, 29, 1, 199, 199, 199, 199] 201
rigid atoms, others: [35, 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, 36, 37, 38, 39])
total number of confs: 743
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052092 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052092
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052092/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052092
Building REAL300025052093
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052093'
/scratch/stefan/7786831/working/building/REAL300025052093 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052093

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052093/0 /scratch/stefan/7786831/working/building/REAL300025052093 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1004)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1004
`/scratch/stefan/7786831/working/3D/1004' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2CC=CCC2)CC1)

`REAL300025052093.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052093.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052093/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052093 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2CC=CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 1, 1, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 18, 50, 60, 133, 133, 133, 133, 133, 5, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 1, 1, 50, 50, 133, 18, 5, 5, 3, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052093 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2CC=CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 1, 1, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [60, 33, 12, 1, 1, 1, 1, 1, 1, 1, 60, 60, 119, 133, 133, 133, 133, 201, 201, 201, 201, 201, 201, 133, 133, 33, 33, 1, 60, 119, 119, 133, 201, 201, 201, 201, 201, 201, 201, 201, 133, 133, 133, 133] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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])
total number of confs: 744
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052093 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)[C@@H]2CC=CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 7, 5, 1, 1, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [65, 65, 65, 135, 148, 201, 201, 201, 201, 201, 21, 15, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 15, 15, 135, 135, 201, 65, 21, 21, 9, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42, 43])
total number of confs: 646
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052093 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052093
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052093/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052093
Building REAL300025052094
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052094'
/scratch/stefan/7786831/working/building/REAL300025052094 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052094

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052094/0 /scratch/stefan/7786831/working/building/REAL300025052094 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1005)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1005
`/scratch/stefan/7786831/working/3D/1005' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052094.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052094.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052094/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052094 none COCC=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 176, 176, 121, 121, 121, 121, 100, 65, 65, 27, 65, 13, 1, 1, 1, 1, 1, 1, 1, 121, 121, 201, 201, 201, 201, 201, 176, 176, 121, 100, 100, 65, 27, 27, 1, 121, 121, 121, 121] 201
rigid atoms, others: [36, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 816
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052094 none COCC=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 19, 7, 7, 2, 2, 2, 1, 1, 1, 4, 6, 6, 6, 24, 42, 121, 121, 121, 121, 121, 1, 1, 28, 28, 28, 19, 19, 7, 7, 2, 4, 4, 6, 24, 24, 121, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 7, 8, 9, 39, 40, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 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])
total number of confs: 310
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052094 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052094
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052094/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052094
Building REAL300025052095
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052095'
/scratch/stefan/7786831/working/building/REAL300025052095 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025052095

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052095/0 /scratch/stefan/7786831/working/building/REAL300025052095 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1006)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1006
`/scratch/stefan/7786831/working/3D/1006' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CC[N@H+](C)CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025052095.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052095.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052095/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052095 none CN1CC[N@H+](C)CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
8  conformations in input
total number of sets (complete confs): 8
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 3, 6, 6, 6, 7, 7, 8, 8, 8, 8, 8, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 6, 7, 7, 8, 1, 1, 1, 1, 3, 3] 8
rigid atoms, others: [11, 12, 13, 48, 49, 50, 51, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 52, 53])
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: REAL300025052095 none CN1CC[N@H+](C)CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 3, 3, 3, 3, 4, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 3, 3, 1, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 3, 4, 4, 7, 7, 7, 8, 3, 3, 3, 3, 1, 1] 8
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 38, 7, 34, 40, 52, 53, 9, 39, 27, 5, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 37
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052095 none CN1CC[N@H+](C)CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 7, 7, 7, 6, 7, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 7, 6, 6, 1, 8, 8, 8, 8, 8, 8] 8
rigid atoms, others: [47, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53])
total number of confs: 20
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052095 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025052095/1 /scratch/stefan/7786831/working/building/REAL300025052095 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 1007)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1007
`/scratch/stefan/7786831/working/3D/1007' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CC[N@@H+](C)CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025052095.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025052095.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052095/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052095 none CN1CC[N@@H+](C)CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
8  conformations in input
total number of sets (complete confs): 8
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 3, 6, 6, 6, 7, 7, 8, 8, 8, 8, 8, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 6, 7, 7, 8, 1, 1, 1, 1, 3, 3] 8
rigid atoms, others: [11, 12, 13, 48, 49, 50, 51, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 52, 53])
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: REAL300025052095 none CN1CC[N@@H+](C)CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 3, 3, 3, 3, 4, 6, 6, 6, 7, 7, 8, 8, 8, 8, 8, 3, 3, 1, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 3, 4, 4, 6, 7, 7, 8, 3, 3, 3, 3, 1, 1] 8
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 38, 7, 34, 40, 52, 53, 9, 39, 27, 5, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 39
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052095 none CN1CC[N@@H+](C)CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 7, 7, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 5, 5, 1, 8, 8, 8, 8, 8, 8] 8
rigid atoms, others: [47, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53])
total number of confs: 18
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052095 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052095
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025052095/1.*
0: /scratch/stefan/7786831/working/building/REAL300025052095/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052095
Building REAL300025052096
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052096'
/scratch/stefan/7786831/working/building/REAL300025052096 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300025052096

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052096/0 /scratch/stefan/7786831/working/building/REAL300025052096 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1008)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1008
`/scratch/stefan/7786831/working/3D/1008' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)[N@@H+]1CCCC(O)C1)

`REAL300025052096.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052096.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052096/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052096 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)[N@@H+]1CCCC(O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 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
189  conformations in input
total number of sets (complete confs): 189
using faster count positions algorithm for large data
unique positions, atoms: [63, 60, 60, 60, 60, 58, 41, 41, 25, 41, 12, 1, 1, 1, 1, 1, 1, 1, 60, 60, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 60, 58, 58, 41, 25, 25, 1, 60, 60, 60, 60, 63, 63, 63, 63, 63, 63, 63, 189, 63, 63] 189
rigid atoms, others: [38, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 435
number of broken/clashed sets: 54
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052096 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)[N@@H+]1CCCC(O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 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
189  conformations in input
total number of sets (complete confs): 189
using faster count positions algorithm for large data
unique positions, atoms: [8, 2, 2, 2, 1, 1, 1, 5, 12, 12, 12, 24, 33, 60, 60, 60, 60, 60, 1, 1, 8, 12, 12, 12, 12, 12, 12, 12, 8, 8, 8, 8, 2, 5, 5, 12, 24, 24, 60, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 36, 12, 12] 189
rigid atoms, others: [4, 5, 6, 39, 40, 41, 42, 18, 19] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 236
number of broken/clashed sets: 54
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052096 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)[N@@H+]1CCCC(O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 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
189  conformations in input
total number of sets (complete confs): 189
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 12, 12, 12, 12, 17, 23, 23, 23, 35, 40, 63, 63, 63, 63, 63, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 12, 17, 17, 23, 35, 35, 63, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1] 189
rigid atoms, others: [1, 43, 44, 45, 46, 47, 48, 49, 51, 20, 21, 22, 23, 24, 25, 26, 27, 52] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 50])
total number of confs: 205
number of broken/clashed sets: 54
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052096 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025052096/1 /scratch/stefan/7786831/working/building/REAL300025052096 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 1009)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1009
`/scratch/stefan/7786831/working/3D/1009' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)[N@H+]1CCCC(O)C1)

`REAL300025052096.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025052096.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052096/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052096 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)[N@H+]1CCCC(O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 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
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [29, 28, 28, 28, 28, 25, 22, 22, 13, 22, 9, 1, 1, 1, 1, 1, 1, 1, 28, 28, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 28, 25, 25, 22, 13, 13, 1, 28, 28, 28, 28, 29, 29, 29, 29, 29, 29, 29, 87, 29, 29] 87
rigid atoms, others: [38, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 189
number of broken/clashed sets: 63
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052096 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)[N@H+]1CCCC(O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 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
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [7, 2, 2, 2, 1, 1, 1, 6, 10, 10, 10, 14, 16, 28, 28, 28, 28, 28, 1, 1, 7, 8, 8, 8, 8, 8, 8, 8, 7, 7, 7, 7, 2, 6, 6, 10, 14, 14, 28, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 24, 8, 8] 87
rigid atoms, others: [4, 5, 6, 39, 40, 41, 42, 18, 19] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 124
number of broken/clashed sets: 63
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052096 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)[N@H+]1CCCC(O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 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
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 8, 8, 8, 8, 11, 14, 14, 14, 18, 19, 29, 29, 29, 29, 29, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 8, 11, 11, 14, 18, 18, 29, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1] 87
rigid atoms, others: [1, 43, 44, 45, 46, 47, 48, 49, 51, 20, 21, 22, 23, 24, 25, 26, 27, 52] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 50])
total number of confs: 95
number of broken/clashed sets: 63
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052096 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `2'
/scratch/stefan/7786831/working/building/REAL300025052096/2 /scratch/stefan/7786831/working/building/REAL300025052096 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 2 (index: 1010)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1010
`/scratch/stefan/7786831/working/3D/1010' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)N1CCCC(O)C1)

`REAL300025052096.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300025052096.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052096/2/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`2.mol2' -> `2.mol2.original'
`output.mol2' -> `2.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052096 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)N1CCCC(O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 144, 144, 144, 144, 102, 54, 54, 30, 54, 13, 1, 1, 1, 1, 1, 1, 1, 144, 144, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 144, 102, 102, 54, 30, 30, 1, 144, 144, 144, 144, 201, 201, 201, 201, 201, 201, 201, 603, 201, 201] 603
rigid atoms, others: [37, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 1444
number of broken/clashed sets: 159
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052096 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)N1CCCC(O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [5, 2, 2, 2, 1, 1, 1, 7, 17, 17, 17, 55, 63, 144, 144, 144, 144, 144, 1, 1, 5, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 2, 7, 7, 17, 55, 55, 144, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 21, 7, 7] 603
rigid atoms, others: [4, 5, 38, 39, 40, 41, 18, 19, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 387
number of broken/clashed sets: 159
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052096 none CC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)N1CCCC(O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 7, 7, 7, 7, 21, 41, 41, 41, 103, 111, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 21, 21, 41, 103, 103, 201, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 6, 1, 1] 603
rigid atoms, others: [1, 42, 43, 44, 45, 46, 47, 48, 50, 51, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 49])
total number of confs: 591
number of broken/clashed sets: 159
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052096 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052096
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
2: /scratch/stefan/7786831/working/building/REAL300025052096/2.*
1: /scratch/stefan/7786831/working/building/REAL300025052096/1.*
0: /scratch/stefan/7786831/working/building/REAL300025052096/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052096
Building REAL300025052097
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052097'
/scratch/stefan/7786831/working/building/REAL300025052097 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052097

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052097/0 /scratch/stefan/7786831/working/building/REAL300025052097 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1011)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1011
`/scratch/stefan/7786831/working/3D/1011' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=NON=C32)CC1)

`REAL300025052097.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052097.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052097/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052097 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=NON=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'N.2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 12, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 80, 87, 201, 201, 201, 201, 201, 7, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 80, 80, 201, 27, 7, 7, 3, 6, 6, 6, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 483
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052097 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=NON=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'N.2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 12, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [62, 34, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 143, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 34, 34, 1, 62, 143, 143, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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])
total number of confs: 742
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052097 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC3=NON=C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'N.2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 12, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [49, 49, 49, 127, 132, 201, 201, 201, 201, 201, 13, 6, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 127, 127, 201, 49, 13, 13, 4, 1, 1, 1, 6, 6, 6, 6] 201
rigid atoms, others: [34, 35, 36, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40])
total number of confs: 616
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052097 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052097
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052097/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052097
Building REAL300025052098
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052098'
/scratch/stefan/7786831/working/building/REAL300025052098 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052098

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052098/0 /scratch/stefan/7786831/working/building/REAL300025052098 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1012)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1012
`/scratch/stefan/7786831/working/3D/1012' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCOC1COC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052098.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052098.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052098/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052098 none O=C(CCOC1COC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 12, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 3, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 9, 9, 21, 48, 48, 48, 1, 1, 1, 3, 5, 5, 5, 16, 25, 70, 70, 70, 70, 70, 1, 1, 9, 9, 9, 9, 48, 48, 48, 48, 48, 2, 3, 3, 5, 16, 16, 70, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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: REAL300025052098 none O=C(CCOC1COC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 12, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 3, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [48, 24, 13, 6, 1, 1, 1, 1, 1, 48, 48, 48, 58, 75, 75, 75, 126, 145, 201, 201, 201, 201, 201, 48, 48, 24, 24, 13, 13, 1, 1, 1, 1, 1, 48, 58, 58, 75, 126, 126, 201, 48, 48, 48, 48] 201
rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 721
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052098 none O=C(CCOC1COC1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 12, 5, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 3, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 150, 150, 154, 201, 201, 201, 70, 61, 46, 46, 27, 46, 12, 1, 1, 1, 1, 1, 1, 1, 70, 70, 150, 150, 150, 150, 201, 201, 201, 201, 201, 70, 61, 61, 46, 27, 27, 1, 70, 70, 70, 70] 201
rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 807
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052098 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052098
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052098/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052098
Building REAL300025052099
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052099'
/scratch/stefan/7786831/working/building/REAL300025052099 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052099

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052099/0 /scratch/stefan/7786831/working/building/REAL300025052099 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1013)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1013
`/scratch/stefan/7786831/working/3D/1013' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: [N-]=[N+]=N[C@H]1C[C@H](C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025052099.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052099.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052099/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052099 none [N-]=[N+]=N[C@H]1C[C@H](C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['N.1', 'N.1', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 8, 8, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 32, 8, 8, 8, 8, 2, 8, 2, 2, 1, 1, 1, 4, 6, 6, 6, 21, 38, 143, 143, 143, 143, 143, 1, 1, 8, 8, 8, 2, 4, 4, 6, 21, 21, 143, 1, 1, 1, 1, 8, 8] 201
rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41])
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: REAL300025052099 none [N-]=[N+]=N[C@H]1C[C@H](C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['N.1', 'N.1', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 8, 8, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 18, 26, 26, 26, 67, 98, 198, 198, 198, 198, 198, 8, 8, 1, 1, 1, 8, 18, 18, 26, 67, 67, 198, 8, 8, 8, 8, 1, 1] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 41, 40, 26, 27, 28] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 507
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052099 none [N-]=[N+]=N[C@H]1C[C@H](C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['N.1', 'N.1', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 8, 8, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 198, 198, 198, 198, 143, 198, 143, 143, 143, 114, 66, 66, 28, 66, 13, 1, 1, 1, 1, 1, 1, 1, 143, 143, 198, 198, 198, 143, 114, 114, 66, 28, 28, 1, 143, 143, 143, 143, 198, 198] 201
rigid atoms, others: [35, 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, 36, 37, 38, 39, 40, 41])
total number of confs: 781
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052099 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052099
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052099/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052099
Building REAL300025052100
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052100'
/scratch/stefan/7786831/working/building/REAL300025052100 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052100

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052100/0 /scratch/stefan/7786831/working/building/REAL300025052100 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1014)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1014
`/scratch/stefan/7786831/working/3D/1014' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)C(C)CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052100.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052100.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052100/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052100 none CC(=O)C(C)CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 199, 201, 193, 199, 187, 123, 123, 123, 123, 97, 73, 73, 29, 73, 13, 1, 1, 1, 1, 1, 1, 1, 123, 123, 201, 201, 201, 199, 199, 199, 199, 196, 196, 187, 187, 123, 97, 97, 73, 29, 29, 1, 123, 123, 123, 123] 201
rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46])
total number of confs: 863
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052100 none CC(=O)C(C)CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 21, 32, 13, 21, 10, 2, 2, 2, 1, 1, 1, 4, 7, 7, 7, 25, 42, 123, 123, 123, 123, 123, 1, 1, 32, 32, 32, 21, 21, 21, 21, 14, 14, 10, 10, 2, 4, 4, 7, 25, 25, 123, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 46, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 378
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052100 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052100
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052100/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052100
Building REAL300025052101
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052101'
/scratch/stefan/7786831/working/building/REAL300025052101 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052101

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052101/0 /scratch/stefan/7786831/working/building/REAL300025052101 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1015)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1015
`/scratch/stefan/7786831/working/3D/1015' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(O)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052101.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052101.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052101/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052101 none CC1=CC=C(O)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 9, 9, 2, 2, 2, 1, 1, 1, 7, 23, 23, 23, 53, 65, 147, 147, 147, 147, 147, 1, 1, 9, 9, 9, 9, 9, 18, 9, 2, 7, 7, 23, 53, 53, 147, 1, 1, 1, 1] 402
rigid atoms, others: [43, 40, 41, 10, 11, 12, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 381
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052101 none CC1=CC=C(O)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 26, 66, 66, 66, 128, 142, 201, 201, 201, 201, 201, 9, 9, 2, 2, 2, 1, 1, 2, 1, 9, 26, 26, 66, 128, 128, 201, 9, 9, 9, 9] 402
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 653
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052101 none CC1=CC=C(O)C=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 147, 147, 147, 147, 100, 50, 50, 26, 50, 13, 1, 1, 1, 1, 1, 1, 1, 147, 147, 201, 201, 201, 201, 201, 402, 201, 147, 100, 100, 50, 26, 26, 1, 147, 147, 147, 147] 402
rigid atoms, others: [39, 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, 40, 41, 42, 43])
total number of confs: 1034
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052101 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052101
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052101/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052101
Building REAL300025052102
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052102'
/scratch/stefan/7786831/working/building/REAL300025052102 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052102

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052102/0 /scratch/stefan/7786831/working/building/REAL300025052102 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1016)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1016
`/scratch/stefan/7786831/working/3D/1016' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=CC=C1)

`REAL300025052102.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052102.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052102/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052102 none COC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 157, 157, 157, 157, 111, 58, 58, 27, 58, 13, 1, 1, 1, 1, 1, 1, 1, 157, 157, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 157, 111, 111, 58, 27, 27, 1, 157, 157, 157, 157, 201, 201, 201, 201, 201] 201
rigid atoms, others: [37, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 820
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052102 none COC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 6, 2, 2, 2, 1, 1, 1, 7, 20, 20, 20, 56, 71, 157, 157, 157, 157, 157, 1, 1, 6, 8, 8, 6, 8, 8, 8, 8, 8, 6, 2, 7, 7, 20, 56, 56, 157, 1, 1, 1, 1, 8, 8, 8, 8, 8] 201
rigid atoms, others: [5, 38, 7, 40, 41, 39, 19, 20, 6] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46])
total number of confs: 402
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052102 none COC(C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 3, 1, 3, 8, 8, 8, 8, 22, 43, 43, 43, 96, 112, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 4, 4, 4, 3, 8, 22, 22, 43, 96, 96, 201, 8, 8, 8, 8, 1, 1, 1, 1, 1] 201
rigid atoms, others: [2, 42, 43, 44, 45, 46, 21, 22, 23, 24, 25, 26] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 580
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052102 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052102
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052102/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052102
Building REAL300025052103
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052103'
/scratch/stefan/7786831/working/building/REAL300025052103 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052103

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052103/0 /scratch/stefan/7786831/working/building/REAL300025052103 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1017)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1017
`/scratch/stefan/7786831/working/3D/1017' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3CC3C2)CC1)

`REAL300025052103.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052103.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052103/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052103 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3CC3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 19, 54, 65, 140, 140, 140, 140, 140, 5, 1, 1, 1, 3, 3, 3, 17, 17, 17, 17, 17, 1, 1, 54, 54, 140, 19, 5, 5, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
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: REAL300025052103 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3CC3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [66, 31, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 124, 140, 140, 140, 140, 201, 201, 201, 201, 201, 140, 140, 31, 31, 1, 66, 124, 124, 140, 201, 201, 201, 201, 201, 201, 201, 201, 201, 140, 140, 140, 140] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 742
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052103 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CC3CC3C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 134, 146, 201, 201, 201, 201, 201, 21, 17, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 17, 17, 134, 134, 201, 67, 21, 21, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43])
total number of confs: 642
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052103 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052103
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052103/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052103
Building REAL300025052104
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052104'
/scratch/stefan/7786831/working/building/REAL300025052104 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052104

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052104/0 /scratch/stefan/7786831/working/building/REAL300025052104 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1018)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1018
`/scratch/stefan/7786831/working/3D/1018' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CN=CN=C2)CC1)

`REAL300025052104.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052104.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052104/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052104 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CN=CN=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 71, 85, 139, 139, 139, 139, 139, 6, 1, 1, 1, 3, 3, 3, 8, 13, 13, 8, 13, 13, 1, 1, 71, 71, 139, 24, 6, 6, 3, 8, 8, 13, 8, 13, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 416
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052104 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CN=CN=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 31, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 113, 139, 139, 139, 139, 201, 201, 201, 201, 201, 201, 139, 139, 31, 31, 1, 67, 113, 113, 139, 201, 201, 201, 201, 201, 139, 139, 139, 139] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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])
total number of confs: 847
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052104 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CN=CN=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 8, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [57, 57, 57, 124, 144, 193, 193, 193, 193, 193, 23, 14, 11, 11, 5, 11, 1, 1, 1, 1, 1, 1, 1, 14, 14, 124, 124, 193, 57, 23, 23, 11, 5, 5, 1, 1, 1, 14, 14, 14, 14] 193
rigid atoms, others: [34, 35, 36, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40])
total number of confs: 610
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052104 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052104
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052104/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052104
Building REAL300025052105
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052105'
/scratch/stefan/7786831/working/building/REAL300025052105 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052105

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052105/0 /scratch/stefan/7786831/working/building/REAL300025052105 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1019)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1019
`/scratch/stefan/7786831/working/3D/1019' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(O)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1)

`REAL300025052105.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052105.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052105/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052105 none CC1=CC=C(O)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 29, 29, 29, 98, 125, 199, 199, 199, 199, 199, 1, 1, 4, 4, 4, 4, 4, 4, 8, 2, 7, 7, 29, 98, 98, 199, 1, 1, 1, 1] 402
rigid atoms, others: [39, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 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: REAL300025052105 none CC1=CC=C(O)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 11, 40, 40, 40, 111, 137, 200, 201, 201, 201, 201, 4, 4, 1, 2, 2, 2, 1, 1, 2, 4, 11, 11, 40, 111, 111, 201, 4, 4, 4, 4] 402
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 25, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 595
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052105 none CC1=CC=C(O)C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 199, 199, 199, 199, 142, 60, 60, 30, 60, 13, 1, 1, 1, 1, 1, 1, 1, 199, 199, 201, 201, 201, 201, 201, 201, 402, 199, 142, 142, 60, 30, 30, 1, 199, 199, 199, 199] 402
rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 1149
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052105 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052105
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052105/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052105
Building REAL300025052106
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052106'
/scratch/stefan/7786831/working/building/REAL300025052106 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052106

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052106/0 /scratch/stefan/7786831/working/building/REAL300025052106 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1020)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1020
`/scratch/stefan/7786831/working/3D/1020' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=NNC(=O)[N-]1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052106.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052106.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052106/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052106 none O=C(CCC1=NNC(=O)[N-]1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
151  conformations in input
total number of sets (complete confs): 151
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 3, 3, 6, 6, 6, 6, 6, 1, 1, 1, 6, 15, 15, 15, 46, 79, 144, 144, 144, 144, 144, 1, 1, 3, 3, 3, 3, 6, 2, 6, 6, 15, 46, 46, 144, 1, 1, 1, 1] 151
rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 339
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052106 none O=C(CCC1=NNC(=O)[N-]1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
151  conformations in input
total number of sets (complete confs): 151
using faster count positions algorithm for large data
unique positions, atoms: [6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 27, 27, 27, 62, 98, 151, 151, 151, 151, 151, 6, 6, 4, 4, 4, 4, 1, 6, 12, 12, 27, 62, 62, 151, 6, 6, 6, 6] 151
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 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])
total number of confs: 409
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052106 none O=C(CCC1=NNC(=O)[N-]1)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
151  conformations in input
total number of sets (complete confs): 151
using faster count positions algorithm for large data
unique positions, atoms: [144, 144, 144, 148, 148, 151, 151, 151, 151, 151, 144, 132, 87, 87, 34, 87, 13, 1, 1, 1, 1, 1, 1, 1, 144, 144, 148, 148, 148, 148, 151, 144, 132, 132, 87, 34, 34, 1, 144, 144, 144, 144] 151
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41])
total number of confs: 582
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052106 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052106
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052106/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052106
Building REAL300025052107
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052107'
/scratch/stefan/7786831/working/building/REAL300025052107 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052107

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052107/0 /scratch/stefan/7786831/working/building/REAL300025052107 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1021)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1021
`/scratch/stefan/7786831/working/3D/1021' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCC(=O)CC2)CC1)

`REAL300025052107.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052107.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052107/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052107 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCC(=O)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 69, 83, 157, 157, 157, 157, 157, 5, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 1, 1, 69, 69, 157, 22, 5, 5, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1] 201
rigid atoms, others: [44, 11, 12, 13, 46, 45, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 424
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052107 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCC(=O)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 33, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 128, 157, 157, 157, 157, 201, 201, 201, 201, 201, 201, 201, 157, 157, 33, 33, 1, 72, 128, 128, 157, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 157, 157, 157, 157] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 731
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052107 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCC(=O)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 142, 156, 201, 201, 201, 201, 201, 21, 14, 9, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 142, 142, 201, 65, 21, 21, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 44, 45, 46, 47])
total number of confs: 653
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052107 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052107
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052107/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052107
Building REAL300025052108
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052108'
/scratch/stefan/7786831/working/building/REAL300025052108 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052108

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052108/0 /scratch/stefan/7786831/working/building/REAL300025052108 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1022)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1022
`/scratch/stefan/7786831/working/3D/1022' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2C3CCC(=O)C32)CC1)

`REAL300025052108.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052108.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052108/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052108 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2C3CCC(=O)C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
172  conformations in input
total number of sets (complete confs): 172
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 27, 98, 106, 168, 168, 168, 168, 168, 6, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 1, 1, 98, 98, 168, 27, 6, 6, 3, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1] 172
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 474
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052108 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2C3CCC(=O)C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
172  conformations in input
total number of sets (complete confs): 172
using faster count positions algorithm for large data
unique positions, atoms: [79, 33, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 148, 168, 168, 168, 168, 172, 172, 172, 172, 172, 172, 168, 168, 33, 33, 1, 79, 148, 148, 168, 172, 172, 172, 172, 172, 172, 172, 168, 168, 168, 168] 172
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 644
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052108 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2C3CCC(=O)C32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
172  conformations in input
total number of sets (complete confs): 172
using faster count positions algorithm for large data
unique positions, atoms: [32, 32, 32, 105, 112, 172, 172, 172, 172, 172, 8, 4, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 105, 105, 172, 32, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 172
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42])
total number of confs: 500
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052108 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052108
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052108/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052108
Building REAL300025052109
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052109'
/scratch/stefan/7786831/working/building/REAL300025052109 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052109

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052109/0 /scratch/stefan/7786831/working/building/REAL300025052109 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1023)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1023
`/scratch/stefan/7786831/working/3D/1023' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C12CC(C(=O)NC3(CNC(=O)CSC4=NNC(=O)[N-]4)CC3)(C1)C2)

`REAL300025052109.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052109.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052109/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052109 none COC(=O)C12CC(C(=O)NC3(CNC(=O)CSC4=NNC(=O)[N-]4)CC3)(C1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 7, 19, 7, 7, 2, 2, 2, 1, 1, 1, 4, 6, 6, 6, 11, 24, 62, 62, 62, 62, 62, 1, 1, 7, 7, 19, 19, 19, 7, 7, 2, 4, 4, 6, 11, 11, 62, 1, 1, 1, 1, 7, 7, 7, 7] 144
rigid atoms, others: [39, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46])
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: REAL300025052109 none COC(=O)C12CC(C(=O)NC3(CNC(=O)CSC4=NNC(=O)[N-]4)CC3)(C1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 6, 6, 7, 7, 13, 16, 16, 16, 26, 47, 92, 92, 92, 92, 92, 7, 7, 1, 1, 6, 6, 6, 1, 1, 7, 13, 13, 16, 26, 26, 92, 7, 7, 7, 7, 1, 1, 1, 1] 144
rigid atoms, others: [2, 4, 5, 6, 7, 43, 44, 45, 46, 25, 26, 30, 31] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 234
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052109 none COC(=O)C12CC(C(=O)NC3(CNC(=O)CSC4=NNC(=O)[N-]4)CC3)(C1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [144, 144, 92, 144, 92, 92, 62, 62, 62, 62, 52, 49, 49, 29, 49, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 92, 92, 144, 144, 144, 92, 92, 62, 52, 52, 49, 29, 29, 1, 62, 62, 62, 62, 92, 92, 92, 92] 144
rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 445
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052109 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052109
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052109/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052109
Building REAL300025052110
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052110'
/scratch/stefan/7786831/working/building/REAL300025052110 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052110

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052110/0 /scratch/stefan/7786831/working/building/REAL300025052110 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1024)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1024
`/scratch/stefan/7786831/working/3D/1024' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=NC=C1C=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052110.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052110.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052110/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052110 none CC1=CC=NC=C1C=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 22, 22, 22, 9, 9, 2, 2, 2, 1, 1, 1, 4, 8, 8, 8, 28, 48, 136, 136, 136, 136, 136, 1, 1, 22, 22, 22, 22, 22, 22, 9, 9, 2, 4, 4, 8, 28, 28, 136, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 42, 11, 12, 13, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 310
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052110 none CC1=CC=NC=C1C=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 20, 20, 22, 39, 59, 59, 59, 112, 138, 201, 201, 201, 201, 201, 22, 22, 2, 2, 2, 1, 1, 1, 6, 6, 22, 39, 39, 59, 112, 112, 201, 22, 22, 22, 22] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 656
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052110 none CC1=CC=NC=C1C=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 173, 173, 136, 136, 136, 136, 109, 64, 64, 29, 64, 12, 1, 1, 1, 1, 1, 1, 1, 136, 136, 201, 201, 201, 201, 201, 201, 173, 173, 136, 109, 109, 64, 29, 29, 1, 136, 136, 136, 136] 201
rigid atoms, others: [41, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 728
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052110 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052110
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052110/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052110
Building REAL300025052111
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052111'
/scratch/stefan/7786831/working/building/REAL300025052111 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052111

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052111/0 /scratch/stefan/7786831/working/building/REAL300025052111 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1025)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1025
`/scratch/stefan/7786831/working/3D/1025' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(Cl)NC2=O)CC1)

`REAL300025052111.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052111.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052111/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052111 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(Cl)NC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 8, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 29, 93, 99, 201, 201, 201, 201, 201, 7, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 1, 1, 93, 93, 201, 29, 7, 7, 3, 5, 5, 5, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 518
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052111 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(Cl)NC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 8, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 35, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 150, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 35, 35, 1, 61, 150, 150, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 769
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052111 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=C(Cl)NC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 8, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 48, 133, 136, 201, 201, 201, 201, 201, 11, 5, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 133, 133, 201, 48, 11, 11, 4, 1, 1, 1, 5, 5, 5, 5] 201
rigid atoms, others: [33, 34, 35, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39])
total number of confs: 631
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052111 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052111
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052111/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052111
Building REAL300025052112
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052112'
/scratch/stefan/7786831/working/building/REAL300025052112 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052112

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052112/0 /scratch/stefan/7786831/working/building/REAL300025052112 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1026)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1026
`/scratch/stefan/7786831/working/3D/1026' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1)

`REAL300025052112.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052112.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052112/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052112 none CNC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 22, 22, 22, 67, 76, 187, 187, 187, 187, 187, 1, 1, 4, 8, 8, 8, 8, 4, 4, 4, 2, 7, 7, 22, 67, 67, 187, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 9, 10, 11, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 449
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052112 none CNC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 10, 27, 27, 27, 78, 88, 201, 201, 201, 201, 201, 4, 4, 1, 4, 4, 4, 3, 1, 1, 1, 4, 10, 10, 27, 78, 78, 201, 4, 4, 4, 4] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 25, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 501
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052112 none CNC1=CC=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 187, 187, 187, 187, 113, 48, 48, 26, 48, 13, 1, 1, 1, 1, 1, 1, 1, 187, 187, 201, 201, 201, 201, 201, 201, 201, 201, 187, 113, 113, 48, 26, 26, 1, 187, 187, 187, 187] 201
rigid atoms, others: [39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 699
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052112 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052112
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052112/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052112
Building REAL300025052113
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052113'
/scratch/stefan/7786831/working/building/REAL300025052113 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052113

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052113/0 /scratch/stefan/7786831/working/building/REAL300025052113 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1027)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1027
`/scratch/stefan/7786831/working/3D/1027' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052113.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052113.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052113/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052113 none CS(=O)CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 14, 11, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 197, 137, 137, 137, 137, 106, 65, 65, 29, 65, 13, 1, 1, 1, 1, 1, 1, 1, 137, 137, 201, 201, 201, 201, 201, 197, 197, 137, 106, 106, 65, 29, 29, 1, 137, 137, 137, 137] 201
rigid atoms, others: [36, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 880
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052113 none CS(=O)CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 14, 11, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 11, 23, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 9, 27, 41, 137, 137, 137, 137, 137, 1, 1, 23, 23, 23, 11, 11, 9, 9, 2, 5, 5, 9, 27, 27, 137, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 7, 8, 9, 39, 40, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 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])
total number of confs: 339
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052113 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052113
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052113/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052113
Building REAL300025052114
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052114'
/scratch/stefan/7786831/working/building/REAL300025052114 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052114

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052114/0 /scratch/stefan/7786831/working/building/REAL300025052114 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1028)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1028
`/scratch/stefan/7786831/working/3D/1028' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C(=O)C2CCCC2)CC1)

`REAL300025052114.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052114.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052114/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052114 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C(=O)C2CCCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
125  conformations in input
total number of sets (complete confs): 125
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 12, 24, 30, 63, 63, 63, 63, 63, 4, 1, 1, 1, 3, 3, 3, 14, 14, 45, 45, 45, 45, 1, 1, 24, 24, 63, 12, 4, 4, 3, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1] 125
rigid atoms, others: [43, 41, 42, 11, 12, 13, 44, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 262
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052114 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C(=O)C2CCCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
125  conformations in input
total number of sets (complete confs): 125
using faster count positions algorithm for large data
unique positions, atoms: [40, 21, 12, 1, 1, 1, 1, 1, 1, 1, 40, 40, 59, 63, 63, 63, 63, 93, 93, 125, 125, 125, 125, 63, 63, 21, 21, 1, 40, 59, 59, 63, 125, 125, 125, 125, 125, 125, 125, 125, 125, 63, 63, 63, 63] 125
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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: 469
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052114 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C(=O)C2CCCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
125  conformations in input
total number of sets (complete confs): 125
using faster count positions algorithm for large data
unique positions, atoms: [84, 84, 84, 102, 112, 125, 125, 125, 125, 125, 53, 45, 39, 38, 11, 38, 1, 11, 1, 1, 1, 1, 1, 45, 45, 102, 102, 125, 84, 53, 53, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45] 125
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44])
total number of confs: 411
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052114 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052114
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052114/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052114
Building REAL300025052115
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052115'
/scratch/stefan/7786831/working/building/REAL300025052115 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052115

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052115/0 /scratch/stefan/7786831/working/building/REAL300025052115 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1029)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1029
`/scratch/stefan/7786831/working/3D/1029' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(F)=N1)

`REAL300025052115.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052115.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052115/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052115 none COC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'F', 'N.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, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 6, 6, 2, 2, 2, 1, 1, 1, 7, 28, 28, 28, 75, 86, 189, 190, 190, 190, 190, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 7, 7, 28, 75, 75, 190, 1, 1, 1, 1] 201
rigid atoms, others: [39, 8, 9, 10, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 476
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052115 none COC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'F', 'N.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, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 20, 57, 57, 57, 123, 132, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 2, 2, 2, 1, 1, 6, 20, 20, 57, 123, 123, 201, 6, 6, 6, 6] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 25, 26, 30, 31] set([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])
total number of confs: 633
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052115 none COC1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C(F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'F', 'N.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, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 190, 190, 190, 123, 46, 46, 25, 46, 13, 1, 1, 1, 1, 1, 1, 1, 190, 190, 201, 201, 201, 201, 201, 201, 201, 201, 190, 123, 123, 46, 25, 25, 1, 190, 190, 190, 190] 201
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42])
total number of confs: 717
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052115 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052115
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052115/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052115
Building REAL300025052116
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052116'
/scratch/stefan/7786831/working/building/REAL300025052116 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052116

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052116/0 /scratch/stefan/7786831/working/building/REAL300025052116 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1030)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1030
`/scratch/stefan/7786831/working/3D/1030' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CN(C)N=C1)

`REAL300025052116.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052116.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052116/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052116 none CC(=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CN(C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [157, 157, 86, 86, 86, 86, 75, 51, 51, 25, 51, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 157, 201, 201, 201, 201, 201, 157, 157, 157, 157, 86, 75, 75, 51, 25, 25, 1, 86, 86, 86, 86, 201, 201, 201, 201, 201] 201
rigid atoms, others: [37, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300025052116 none CC(=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CN(C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 2, 2, 2, 1, 1, 1, 3, 5, 5, 5, 17, 28, 86, 86, 86, 86, 86, 1, 1, 7, 32, 32, 32, 32, 32, 7, 7, 7, 7, 2, 3, 3, 5, 17, 17, 86, 1, 1, 1, 1, 32, 32, 32, 32, 32] 201
rigid atoms, others: [5, 38, 7, 40, 41, 39, 19, 20, 6] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46])
total number of confs: 213
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052116 none CC(=CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)C1=CN(C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 32, 32, 32, 32, 49, 69, 69, 69, 109, 137, 201, 201, 201, 201, 201, 32, 32, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 32, 49, 49, 69, 109, 109, 201, 32, 32, 32, 32, 1, 2, 2, 2, 1] 201
rigid atoms, others: [1, 42, 46, 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, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45])
total number of confs: 660
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052116 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052116
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052116/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052116
Building REAL300025052117
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052117'
/scratch/stefan/7786831/working/building/REAL300025052117 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052117

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052117/0 /scratch/stefan/7786831/working/building/REAL300025052117 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1031)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1031
`/scratch/stefan/7786831/working/3D/1031' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=CC(F)=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1F)

`REAL300025052117.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052117.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052117/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052117 none NC1=CC(F)=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1F NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 15, 6, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 3, 5, 5, 5, 2, 2, 2, 1, 1, 1, 7, 24, 24, 24, 72, 82, 186, 187, 187, 187, 187, 1, 1, 5, 5, 5, 5, 5, 5, 2, 7, 7, 24, 72, 72, 187, 1, 1, 1, 1, 5] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 40, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: REAL300025052117 none NC1=CC(F)=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1F NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 15, 6, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 18, 54, 54, 54, 127, 134, 200, 201, 201, 201, 201, 5, 5, 1, 1, 1, 2, 2, 1, 5, 18, 18, 54, 127, 127, 201, 5, 5, 5, 5, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 24, 25, 26, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 630
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052117 none NC1=CC(F)=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1F NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 15, 6, 6, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 187, 187, 187, 187, 115, 46, 46, 27, 46, 13, 1, 1, 1, 1, 1, 1, 1, 187, 187, 201, 201, 201, 201, 201, 201, 187, 115, 115, 46, 27, 27, 1, 187, 187, 187, 187, 201] 201
rigid atoms, others: [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, 34, 35, 37, 38, 39, 40, 41])
total number of confs: 738
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052117 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052117
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052117/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052117
Building REAL300025052118
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052118'
/scratch/stefan/7786831/working/building/REAL300025052118 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052118

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052118/0 /scratch/stefan/7786831/working/building/REAL300025052118 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1032)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1032
`/scratch/stefan/7786831/working/3D/1032' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1F)

`REAL300025052118.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052118.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052118/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052118 none CN1N=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'F', '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, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 15, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 30, 30, 30, 97, 120, 201, 201, 201, 201, 201, 1, 1, 4, 4, 4, 4, 4, 4, 2, 7, 7, 30, 97, 97, 201, 1, 1, 1, 1, 4] 201
rigid atoms, others: [35, 36, 37, 6, 7, 8, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39])
total number of confs: 547
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052118 none CN1N=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'F', '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, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 15, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 37, 37, 37, 102, 125, 201, 201, 201, 201, 201, 4, 4, 1, 1, 1, 2, 2, 2, 4, 10, 10, 37, 102, 102, 201, 4, 4, 4, 4, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 39, 22, 23, 24] set([5, 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, 36, 37, 38])
total number of confs: 557
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052118 none CN1N=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'F', '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, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 15, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 137, 56, 56, 28, 56, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 137, 137, 56, 28, 28, 1, 201, 201, 201, 201, 201] 201
rigid atoms, others: [34, 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, 35, 36, 37, 38, 39])
total number of confs: 760
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052118 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052118
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052118/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052118
Building REAL300025052119
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052119'
/scratch/stefan/7786831/working/building/REAL300025052119 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052119

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052119/0 /scratch/stefan/7786831/working/building/REAL300025052119 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1033)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1033
`/scratch/stefan/7786831/working/3D/1033' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=NN1CCCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052119.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052119.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052119/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052119 none O=NN1CCCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 8, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 5, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 6, 19, 19, 19, 57, 89, 181, 181, 181, 181, 181, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 6, 6, 19, 57, 57, 181, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 10, 11, 12, 45, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 441
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052119 none O=NN1CCCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 8, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 30, 30, 30, 84, 122, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 30, 84, 84, 201, 5, 5, 5, 5] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 26, 27, 28, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 541
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052119 none O=NN1CCCCC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 8, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 181, 181, 181, 181, 144, 76, 76, 32, 76, 13, 1, 1, 1, 1, 1, 1, 1, 181, 181, 201, 201, 201, 201, 201, 201, 201, 201, 201, 181, 144, 144, 76, 32, 32, 1, 181, 181, 181, 181] 201
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 784
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052119 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052119
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052119/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052119
Building REAL300025052120
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052120'
/scratch/stefan/7786831/working/building/REAL300025052120 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052120

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052120/0 /scratch/stefan/7786831/working/building/REAL300025052120 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1034)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1034
`/scratch/stefan/7786831/working/3D/1034' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=C(Cl)Cl)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052120.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052120.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052120/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052120 none O=C(C=C(Cl)Cl)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'Cl', 'Cl', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 16, 16, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [160, 160, 160, 201, 201, 201, 160, 141, 83, 83, 36, 83, 13, 1, 1, 1, 1, 1, 1, 1, 160, 160, 201, 160, 141, 141, 83, 36, 36, 1, 160, 160, 160, 160] 201
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33])
total number of confs: 762
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052120 none O=C(C=C(Cl)Cl)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'Cl', 'Cl', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 16, 16, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 7, 7, 7, 1, 1, 1, 6, 22, 22, 22, 72, 94, 160, 160, 160, 160, 160, 1, 1, 7, 2, 6, 6, 22, 72, 72, 160, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 6, 7, 8, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 420
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052120 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052120
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052120/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052120
Building REAL300025052121
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052121'
/scratch/stefan/7786831/working/building/REAL300025052121 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052121

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052121/0 /scratch/stefan/7786831/working/building/REAL300025052121 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1035)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1035
`/scratch/stefan/7786831/working/3D/1035' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSC1=CC=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1)

`REAL300025052121.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052121.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052121/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052121 none CSC1=CC=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 7, 7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 4, 10, 10, 10, 33, 57, 155, 155, 155, 155, 155, 1, 1, 7, 19, 19, 19, 7, 7, 2, 4, 4, 10, 33, 33, 155, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 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: REAL300025052121 none CSC1=CC=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 16, 29, 29, 29, 80, 120, 201, 201, 201, 201, 201, 7, 7, 1, 8, 8, 8, 1, 1, 7, 16, 16, 29, 80, 80, 201, 7, 7, 7, 7] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 25, 29, 30] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 553
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052121 none CSC1=CC=NC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 155, 155, 155, 155, 135, 74, 74, 29, 74, 13, 1, 1, 1, 1, 1, 1, 1, 155, 155, 201, 201, 201, 201, 201, 201, 155, 135, 135, 74, 29, 29, 1, 155, 155, 155, 155] 201
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41])
total number of confs: 699
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052121 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052121
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052121/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052121
Building REAL300025052122
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052122'
/scratch/stefan/7786831/working/building/REAL300025052122 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052122

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052122/0 /scratch/stefan/7786831/working/building/REAL300025052122 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1036)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1036
`/scratch/stefan/7786831/working/3D/1036' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C[N-]N=CC2=O)CC1)

`REAL300025052122.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052122.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052122/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052122 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C[N-]N=CC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [22, 22, 22, 62, 106, 173, 173, 173, 173, 173, 6, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 1, 1, 62, 62, 173, 22, 6, 6, 3, 14, 13, 1, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33])
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: REAL300025052122 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C[N-]N=CC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [97, 39, 13, 1, 1, 1, 1, 1, 1, 1, 97, 97, 159, 173, 176, 176, 176, 201, 201, 201, 201, 201, 201, 173, 173, 39, 39, 1, 97, 159, 159, 176, 201, 201, 173, 173, 173, 173] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 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])
total number of confs: 713
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052122 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=C[N-]N=CC2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 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: [51, 51, 51, 101, 147, 201, 201, 201, 201, 201, 24, 14, 9, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 14, 101, 101, 201, 51, 24, 24, 9, 1, 1, 14, 14, 14, 14] 201
rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37])
total number of confs: 584
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052122 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052122
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052122/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052122
Building REAL300025052123
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052123'
/scratch/stefan/7786831/working/building/REAL300025052123 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025052123

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052123/0 /scratch/stefan/7786831/working/building/REAL300025052123 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1037)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1037
`/scratch/stefan/7786831/working/3D/1037' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@@H+]1CCCC(O)(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025052123.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052123.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052123/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052123 none C[N@@H+]1CCCC(O)(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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, 7, 7, 7, 7, 7, 5, 7, 2, 2, 2, 1, 1, 1, 5, 8, 8, 8, 16, 22, 39, 39, 39, 39, 39, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 21, 5, 5, 2, 5, 5, 8, 16, 16, 39, 1, 1, 1, 1, 7, 7] 117
rigid atoms, others: [11, 12, 13, 47, 48, 49, 50, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52])
total number of confs: 141
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052123 none C[N@@H+]1CCCC(O)(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
117  conformations in input
total number of sets (complete confs): 117
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 9, 10, 10, 10, 18, 25, 39, 39, 39, 39, 39, 7, 7, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 5, 5, 7, 9, 9, 10, 18, 18, 39, 7, 7, 7, 7, 1, 1] 117
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 35, 52, 36, 33, 27, 51, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 122
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052123 none C[N@@H+]1CCCC(O)(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 37, 37, 37, 23, 37, 12, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 117, 39, 39, 39, 37, 37, 37, 23, 23, 1, 39, 39, 39, 39, 39, 39] 117
rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52])
total number of confs: 243
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052123 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025052123/1 /scratch/stefan/7786831/working/building/REAL300025052123 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 1038)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1038
`/scratch/stefan/7786831/working/3D/1038' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@H+]1CCCC(O)(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025052123.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025052123.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052123/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052123 none C[N@H+]1CCCC(O)(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 8, 15, 26, 26, 26, 26, 26, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 4, 4, 2, 4, 4, 4, 8, 8, 26, 1, 1, 1, 1, 4, 4] 78
rigid atoms, others: [11, 12, 13, 47, 48, 49, 50, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52])
total number of confs: 86
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: REAL300025052123 none C[N@H+]1CCCC(O)(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 15, 26, 26, 26, 26, 26, 4, 4, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 4, 4, 4, 4, 4, 4, 8, 8, 26, 4, 4, 4, 4, 1, 1] 78
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 35, 52, 36, 33, 27, 51, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 73
number of broken/clashed sets: 78
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052123 none C[N@H+]1CCCC(O)(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 14, 26, 10, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 78, 26, 26, 26, 26, 26, 26, 14, 14, 1, 26, 26, 26, 26, 26, 26] 78
rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52])
total number of confs: 159
number of broken/clashed sets: 78
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052123 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052123
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025052123/1.*
0: /scratch/stefan/7786831/working/building/REAL300025052123/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052123
Building REAL300025052124
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052124'
/scratch/stefan/7786831/working/building/REAL300025052124 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052124

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052124/0 /scratch/stefan/7786831/working/building/REAL300025052124 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1039)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1039
`/scratch/stefan/7786831/working/3D/1039' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C(C#N)N1)

`REAL300025052124.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052124.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052124/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052124 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C(C#N)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.1', 'N.1', 'N.pl3', '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, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 8, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 2, 2, 1, 1, 1, 7, 25, 25, 25, 61, 72, 147, 147, 147, 147, 147, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 2, 7, 7, 25, 61, 61, 147, 1, 1, 1, 1, 9, 9] 201
rigid atoms, others: [36, 5, 6, 7, 39, 19, 20, 38, 37] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41])
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: REAL300025052124 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C(C#N)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.1', 'N.1', 'N.pl3', '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, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 8, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 8, 9, 9, 27, 64, 64, 64, 117, 128, 201, 201, 201, 201, 201, 9, 9, 1, 1, 1, 1, 1, 2, 2, 2, 9, 27, 27, 64, 117, 117, 201, 9, 9, 9, 9, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 40, 41, 21, 22, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 617
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052124 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C=C(C#N)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.1', 'N.1', 'N.pl3', '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, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 8, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 147, 147, 147, 147, 99, 48, 48, 26, 48, 13, 1, 1, 1, 1, 1, 1, 1, 147, 147, 201, 201, 201, 201, 201, 201, 201, 201, 147, 99, 99, 48, 26, 26, 1, 147, 147, 147, 147, 201, 201] 201
rigid atoms, others: [35, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41])
total number of confs: 637
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052124 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052124
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052124/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052124
Building REAL300025052125
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052125'
/scratch/stefan/7786831/working/building/REAL300025052125 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052125

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052125/0 /scratch/stefan/7786831/working/building/REAL300025052125 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1040)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1040
`/scratch/stefan/7786831/working/3D/1040' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1)

`REAL300025052125.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052125.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052125/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052125 none COC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 30, 30, 30, 92, 110, 201, 201, 201, 201, 201, 1, 1, 4, 4, 4, 4, 4, 2, 7, 7, 30, 92, 92, 201, 1, 1, 1, 1, 4] 201
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40])
total number of confs: 543
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052125 none COC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 15, 47, 47, 47, 111, 127, 201, 201, 201, 201, 201, 4, 4, 1, 2, 2, 2, 1, 4, 15, 15, 47, 111, 111, 201, 4, 4, 4, 4, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 24, 28] set([0, 7, 8, 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])
total number of confs: 594
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052125 none COC1=NNC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 137, 56, 56, 31, 56, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 137, 137, 56, 31, 31, 1, 201, 201, 201, 201, 201] 201
rigid atoms, others: [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, 33, 34, 36, 37, 38, 39, 40])
total number of confs: 758
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052125 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052125
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052125/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052125
Building REAL300025052126
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052126'
/scratch/stefan/7786831/working/building/REAL300025052126 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052126

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052126/0 /scratch/stefan/7786831/working/building/REAL300025052126 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1041)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1041
`/scratch/stefan/7786831/working/3D/1041' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCC(C)(C)C1)

`REAL300025052126.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052126.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052126/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052126 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCC(C)(C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 2, 1, 1, 1, 7, 23, 23, 23, 69, 76, 151, 151, 151, 151, 151, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 23, 69, 69, 151, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 201
rigid atoms, others: [37, 6, 7, 40, 39, 19, 20, 38, 5] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 410
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052126 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCC(C)(C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 4, 12, 42, 42, 42, 106, 114, 201, 201, 201, 201, 201, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 12, 12, 42, 106, 106, 201, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 44, 51, 52, 21, 22, 23, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 50])
total number of confs: 587
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052126 none CC1=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCC(C)(C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 151, 151, 151, 151, 98, 44, 44, 27, 44, 13, 1, 1, 1, 1, 1, 1, 1, 151, 151, 201, 201, 201, 201, 201, 201, 201, 201, 201, 151, 98, 98, 44, 27, 27, 1, 151, 151, 151, 151, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [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, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 669
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052126 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052126
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052126/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052126
Building REAL300025052127
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052127'
/scratch/stefan/7786831/working/building/REAL300025052127 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025052127

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052127/0 /scratch/stefan/7786831/working/building/REAL300025052127 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1042)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1042
`/scratch/stefan/7786831/working/3D/1042' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025052127.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052127.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052127/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052127 none CC1CN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 7, 2, 2, 2, 1, 1, 1, 7, 16, 16, 16, 55, 69, 162, 162, 162, 162, 162, 1, 1, 10, 10, 10, 10, 10, 10, 10, 7, 7, 2, 7, 7, 16, 55, 55, 162, 1, 1, 1, 1, 10, 10] 201
rigid atoms, others: [39, 8, 9, 42, 7, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 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, 43, 44])
total number of confs: 410
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052127 none CC1CN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 5, 10, 10, 10, 10, 25, 43, 43, 43, 106, 126, 201, 201, 201, 201, 201, 10, 10, 1, 2, 2, 2, 1, 1, 1, 5, 5, 10, 25, 25, 43, 106, 106, 201, 10, 10, 10, 10, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 43, 44, 23, 27, 28, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 628
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052127 none CC1CN(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 162, 162, 162, 162, 118, 63, 63, 31, 63, 13, 1, 1, 1, 1, 1, 1, 1, 162, 162, 201, 201, 201, 201, 201, 201, 201, 201, 201, 162, 118, 118, 63, 31, 31, 1, 162, 162, 162, 162, 201, 201] 201
rigid atoms, others: [38, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44])
total number of confs: 849
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052127 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025052127/1 /scratch/stefan/7786831/working/building/REAL300025052127 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 1043)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1043
`/scratch/stefan/7786831/working/3D/1043' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C[NH+](CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025052127.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025052127.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052127/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052127 none CC1C[NH+](CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 8, 13, 2, 2, 2, 1, 1, 1, 5, 10, 10, 10, 27, 38, 76, 76, 76, 76, 76, 1, 1, 13, 13, 13, 13, 13, 13, 13, 8, 8, 2, 5, 5, 10, 27, 27, 76, 1, 1, 1, 1, 13, 13] 81
rigid atoms, others: [8, 9, 10, 43, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 44, 45])
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: REAL300025052127 none CC1C[NH+](CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 13, 17, 30, 30, 30, 46, 57, 81, 81, 81, 81, 81, 13, 13, 1, 2, 2, 2, 1, 1, 1, 5, 5, 13, 17, 17, 30, 46, 46, 81, 13, 13, 13, 13, 1, 1] 81
rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 45, 24, 28, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 256
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052127 none CC1C[NH+](CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 80, 81, 76, 76, 76, 76, 69, 60, 60, 29, 60, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 81, 81, 81, 81, 81, 81, 81, 80, 80, 76, 69, 69, 60, 29, 29, 1, 76, 76, 76, 76, 81, 81] 81
rigid atoms, others: [39, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45])
total number of confs: 290
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052127 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052127
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025052127/1.*
0: /scratch/stefan/7786831/working/building/REAL300025052127/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052127
Building REAL300025052128
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052128'
/scratch/stefan/7786831/working/building/REAL300025052128 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052128

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052128/0 /scratch/stefan/7786831/working/building/REAL300025052128 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1044)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1044
`/scratch/stefan/7786831/working/3D/1044' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=NC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052128.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052128.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052128/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052128 none COC1=CC=NC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 12, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 5, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 6, 20, 20, 20, 62, 75, 181, 181, 181, 181, 181, 1, 1, 7, 7, 7, 5, 5, 5, 2, 6, 6, 20, 62, 62, 181, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 10, 11, 12, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 417
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052128 none COC1=CC=NC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 12, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 42, 42, 42, 110, 123, 201, 201, 201, 201, 201, 5, 5, 4, 4, 4, 1, 1, 1, 5, 13, 13, 42, 110, 110, 201, 5, 5, 5, 5] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 9, 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, 41, 42])
total number of confs: 588
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052128 none COC1=CC=NC=C1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 12, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 181, 181, 181, 181, 123, 54, 54, 28, 54, 13, 1, 1, 1, 1, 1, 1, 1, 181, 181, 201, 201, 201, 201, 201, 201, 181, 123, 123, 54, 28, 28, 1, 181, 181, 181, 181] 201
rigid atoms, others: [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, 36, 37, 39, 40, 41, 42])
total number of confs: 733
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052128 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052128
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052128/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052128
Building REAL300025052129
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052129'
/scratch/stefan/7786831/working/building/REAL300025052129 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025052129

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052129/0 /scratch/stefan/7786831/working/building/REAL300025052129 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1045)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1045
`/scratch/stefan/7786831/working/3D/1045' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC(F)=C2[O-])CC1)

`REAL300025052129.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052129.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052129/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052129 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC(F)=C2[O-])CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 67, 109, 192, 192, 192, 192, 192, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 1, 1, 67, 67, 192, 22, 6, 6, 3, 7, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 477
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052129 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC(F)=C2[O-])CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 36, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 166, 192, 199, 199, 199, 201, 201, 201, 201, 201, 201, 201, 192, 192, 36, 36, 1, 89, 166, 166, 199, 201, 201, 201, 192, 192, 192, 192] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 786
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052129 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC(F)=C2[O-])CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [39, 39, 39, 89, 133, 201, 201, 201, 201, 201, 16, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 89, 89, 201, 39, 16, 16, 4, 1, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [33, 34, 35, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39])
total number of confs: 558
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052129 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025052129/1 /scratch/stefan/7786831/working/building/REAL300025052129 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 1046)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1046
`/scratch/stefan/7786831/working/3D/1046' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC(F)=C2O)CC1)

`REAL300025052129.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025052129.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052129/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052129 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC(F)=C2O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
386  conformations in input
total number of sets (complete confs): 386
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 27, 91, 113, 170, 170, 170, 170, 170, 6, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 1, 1, 91, 91, 170, 27, 6, 6, 3, 13, 13, 13, 26, 1, 1, 1, 1] 386
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 512
number of broken/clashed sets: 65
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052129 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC(F)=C2O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
386  conformations in input
total number of sets (complete confs): 386
using faster count positions algorithm for large data
unique positions, atoms: [78, 33, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 138, 170, 170, 170, 170, 193, 193, 193, 193, 193, 193, 193, 170, 170, 33, 33, 1, 78, 138, 138, 170, 193, 193, 193, 386, 170, 170, 170, 170] 386
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 1060
number of broken/clashed sets: 65
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052129 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC=CC(F)=C2O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 12, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
386  conformations in input
total number of sets (complete confs): 386
using faster count positions algorithm for large data
unique positions, atoms: [69, 69, 69, 144, 159, 193, 193, 193, 193, 193, 23, 13, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 144, 144, 193, 69, 23, 23, 9, 1, 1, 1, 2, 13, 13, 13, 13] 386
rigid atoms, others: [33, 34, 35, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40])
total number of confs: 638
number of broken/clashed sets: 65
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052129 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052129
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025052129/1.*
0: /scratch/stefan/7786831/working/building/REAL300025052129/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052129
Building REAL300025052130
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052130'
/scratch/stefan/7786831/working/building/REAL300025052130 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052130

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052130/0 /scratch/stefan/7786831/working/building/REAL300025052130 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1047)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1047
`/scratch/stefan/7786831/working/3D/1047' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C(O)C2CCOCC2)CC1)

`REAL300025052130.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052130.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052130/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052130 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C(O)C2CCOCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 12, 37, 48, 125, 125, 125, 125, 125, 5, 1, 1, 1, 3, 3, 3, 18, 18, 32, 32, 32, 32, 32, 1, 1, 37, 37, 125, 12, 5, 5, 3, 18, 54, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1] 603
rigid atoms, others: [44, 11, 12, 13, 46, 45, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 426
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: REAL300025052130 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C(O)C2CCOCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [70, 32, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 113, 125, 125, 125, 125, 181, 181, 201, 201, 201, 201, 201, 125, 125, 32, 32, 1, 70, 113, 113, 125, 181, 543, 201, 201, 201, 201, 201, 201, 201, 201, 201, 125, 125, 125, 125] 603
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 1380
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052130 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C(O)C2CCOCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [79, 79, 79, 128, 143, 201, 201, 201, 201, 201, 43, 32, 22, 22, 6, 22, 1, 6, 1, 1, 1, 1, 1, 1, 32, 32, 128, 128, 201, 79, 43, 43, 22, 6, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32] 603
rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47])
total number of confs: 658
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052130 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052130
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052130/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052130
Building REAL300025052131
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052131'
/scratch/stefan/7786831/working/building/REAL300025052131 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025052131

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052131/0 /scratch/stefan/7786831/working/building/REAL300025052131 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1048)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1048
`/scratch/stefan/7786831/working/3D/1048' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[N@@H+]1CCCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025052131.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052131.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052131/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052131 none CC[N@@H+]1CCCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 3, 5, 5, 5, 9, 11, 13, 13, 13, 13, 13, 1, 1, 4, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 2, 3, 3, 5, 9, 9, 13, 1, 1, 1, 1, 4, 4] 13
rigid atoms, others: [10, 11, 12, 46, 47, 48, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51])
total number of confs: 63
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: REAL300025052131 none CC[N@@H+]1CCCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 6, 9, 11, 13, 13, 13, 13, 13, 4, 4, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 6, 9, 9, 13, 4, 4, 4, 4, 1, 1] 13
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 7, 34, 50, 35, 36, 26, 38, 51, 37] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 49
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052131 none CC[N@@H+]1CCCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 11, 11, 10, 11, 7, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 11, 10, 10, 1, 13, 13, 13, 13, 13, 13] 13
rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51])
total number of confs: 42
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052131 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025052131/1 /scratch/stefan/7786831/working/building/REAL300025052131 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 1049)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1049
`/scratch/stefan/7786831/working/3D/1049' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[N@H+]1CCCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025052131.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025052131.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052131/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052131 none CC[N@H+]1CCCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [5, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 3, 6, 6, 6, 9, 14, 22, 22, 22, 22, 22, 1, 1, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 6, 9, 9, 22, 1, 1, 1, 1, 3, 3] 23
rigid atoms, others: [10, 11, 12, 46, 47, 48, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51])
total number of confs: 78
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: REAL300025052131 none CC[N@H+]1CCCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 11, 11, 11, 13, 15, 23, 23, 23, 23, 23, 3, 3, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 11, 13, 13, 23, 3, 3, 3, 3, 1, 1] 23
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 7, 34, 50, 35, 36, 26, 38, 51, 37] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 77
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052131 none CC[N@H+]1CCCC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 22, 22, 22, 22, 22, 19, 19, 15, 19, 8, 1, 1, 1, 1, 1, 1, 1, 22, 22, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 22, 22, 22, 19, 15, 15, 1, 22, 22, 22, 22, 23, 23] 23
rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51])
total number of confs: 78
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052131 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052131
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
1: /scratch/stefan/7786831/working/building/REAL300025052131/1.*
0: /scratch/stefan/7786831/working/building/REAL300025052131/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052131
Building REAL300025052132
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052132'
/scratch/stefan/7786831/working/building/REAL300025052132 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052132

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052132/0 /scratch/stefan/7786831/working/building/REAL300025052132 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1050)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1050
`/scratch/stefan/7786831/working/3D/1050' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCC(=CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1)

`REAL300025052132.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052132.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052132/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052132 none CC1CCC(=CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 10, 10, 2, 2, 2, 1, 1, 1, 6, 18, 18, 18, 39, 43, 120, 120, 120, 120, 120, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 6, 6, 18, 39, 39, 120, 1, 1, 1, 1, 10, 10] 201
rigid atoms, others: [43, 8, 9, 10, 23, 44, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 45, 46])
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: REAL300025052132 none CC1CCC(=CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 10, 10, 32, 64, 64, 64, 115, 124, 201, 201, 201, 201, 201, 10, 10, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 10, 32, 32, 64, 115, 115, 201, 10, 10, 10, 10, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 45, 46, 24, 33, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 633
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052132 none CC1CCC(=CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 120, 120, 120, 120, 89, 43, 43, 26, 43, 12, 1, 1, 1, 1, 1, 1, 1, 120, 120, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 120, 89, 89, 43, 26, 26, 1, 120, 120, 120, 120, 201, 201] 201
rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46])
total number of confs: 711
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052132 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052132
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052132/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052132
Building REAL300025052133
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052133'
/scratch/stefan/7786831/working/building/REAL300025052133 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052133

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052133/0 /scratch/stefan/7786831/working/building/REAL300025052133 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1051)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1051
`/scratch/stefan/7786831/working/3D/1051' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1CCCCC1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052133.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052133.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052133/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052133 none CC(OC1CCCCC1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 2, 5, 13, 22, 22, 22, 22, 22, 2, 2, 1, 1, 1, 5, 8, 8, 8, 28, 44, 108, 108, 108, 108, 108, 1, 1, 5, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 2, 5, 5, 8, 28, 28, 108, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 49, 50, 51, 52, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
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: REAL300025052133 none CC(OC1CCCCC1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 4, 1, 1, 1, 1, 1, 1, 1, 10, 22, 22, 22, 22, 39, 57, 57, 57, 105, 134, 201, 201, 201, 201, 201, 22, 22, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 39, 39, 57, 105, 105, 201, 22, 22, 22, 22] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 41, 39, 34, 40, 35, 36, 38, 37, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 638
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052133 none CC(OC1CCCCC1)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [156, 108, 156, 180, 201, 201, 201, 201, 201, 108, 108, 108, 95, 56, 56, 26, 56, 13, 1, 1, 1, 1, 1, 1, 1, 108, 108, 156, 156, 156, 156, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 108, 95, 95, 56, 26, 26, 1, 108, 108, 108, 108] 201
rigid atoms, others: [48, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52])
total number of confs: 804
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052133 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052133
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052133/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052133
Building REAL300025052134
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052134'
/scratch/stefan/7786831/working/building/REAL300025052134 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052134

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052134/0 /scratch/stefan/7786831/working/building/REAL300025052134 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1052)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1052
`/scratch/stefan/7786831/working/3D/1052' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C(=O)CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052134.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052134.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052134/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052134 none CN(C)C(=O)CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 197, 149, 149, 149, 149, 121, 77, 77, 32, 77, 13, 1, 1, 1, 1, 1, 1, 1, 149, 149, 201, 201, 201, 201, 201, 201, 201, 201, 197, 197, 149, 121, 121, 77, 32, 32, 1, 149, 149, 149, 149] 201
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 832
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052134 none CN(C)C(=O)CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 12, 16, 9, 2, 2, 2, 1, 1, 1, 5, 12, 12, 12, 37, 62, 149, 149, 149, 149, 149, 1, 1, 16, 16, 16, 16, 16, 16, 12, 12, 9, 9, 2, 5, 5, 12, 37, 37, 149, 1, 1, 1, 1] 201
rigid atoms, others: [43, 9, 10, 11, 44, 45, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 374
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052134 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052134
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052134/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052134
Building REAL300025052135
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052135'
/scratch/stefan/7786831/working/building/REAL300025052135 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052135

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052135/0 /scratch/stefan/7786831/working/building/REAL300025052135 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1053)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1053
`/scratch/stefan/7786831/working/3D/1053' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCC(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052135.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052135.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052135/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052135 none C#CCC(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 178, 124, 178, 124, 124, 124, 106, 65, 65, 26, 65, 11, 1, 1, 1, 1, 1, 1, 1, 124, 124, 201, 201, 201, 178, 178, 178, 178, 124, 106, 106, 65, 26, 26, 1, 124, 124, 124, 124] 201
rigid atoms, others: [36, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 903
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052135 none C#CCC(C)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 7, 2, 7, 2, 2, 1, 1, 1, 5, 9, 9, 9, 30, 47, 124, 124, 124, 124, 124, 1, 1, 17, 17, 17, 7, 7, 7, 7, 2, 5, 5, 9, 30, 30, 124, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 7, 8, 9, 39, 40, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 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])
total number of confs: 322
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052135 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052135
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052135/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052135
Building REAL300025052136
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052136'
/scratch/stefan/7786831/working/building/REAL300025052136 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052136

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052136/0 /scratch/stefan/7786831/working/building/REAL300025052136 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1054)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1054
`/scratch/stefan/7786831/working/3D/1054' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CNC=C(Cl)C2=O)CC1)

`REAL300025052136.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052136.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052136/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052136 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CNC=C(Cl)C2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 16, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 97, 106, 201, 201, 201, 201, 201, 7, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 1, 1, 97, 97, 201, 28, 7, 7, 3, 5, 5, 5, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
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: REAL300025052136 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CNC=C(Cl)C2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 16, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [68, 34, 13, 1, 1, 1, 1, 1, 1, 1, 68, 68, 152, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 34, 34, 1, 68, 152, 152, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 759
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052136 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CNC=C(Cl)C2=O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 16, 1, 11, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 48, 139, 146, 201, 201, 201, 201, 201, 11, 5, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 139, 139, 201, 48, 11, 11, 4, 1, 1, 1, 5, 5, 5, 5] 201
rigid atoms, others: [33, 34, 35, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39])
total number of confs: 637
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052136 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052136
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052136/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052136
Building REAL300025052137
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052137'
/scratch/stefan/7786831/working/building/REAL300025052137 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052137

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052137/0 /scratch/stefan/7786831/working/building/REAL300025052137 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1055)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1055
`/scratch/stefan/7786831/working/3D/1055' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=NC=CC=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052137.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052137.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052137/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052137 none NC1=NC=CC=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 8, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 21, 21, 21, 21, 21, 12, 2, 2, 2, 1, 1, 1, 7, 16, 16, 16, 43, 59, 137, 137, 137, 137, 137, 1, 1, 21, 21, 21, 21, 21, 12, 12, 2, 7, 7, 16, 43, 43, 137, 1, 1, 1, 1] 201
rigid atoms, others: [43, 40, 41, 10, 11, 12, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 361
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052137 none NC1=NC=CC=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 8, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 21, 21, 21, 21, 37, 53, 53, 53, 97, 125, 201, 201, 201, 201, 201, 21, 21, 1, 1, 1, 1, 1, 5, 5, 21, 37, 37, 53, 97, 97, 201, 21, 21, 21, 21] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 26, 27, 28, 29, 30] set([8, 9, 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, 40, 41, 42, 43])
total number of confs: 596
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052137 none NC1=NC=CC=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 8, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 181, 137, 137, 137, 137, 111, 55, 55, 28, 55, 13, 1, 1, 1, 1, 1, 1, 1, 137, 137, 201, 201, 201, 201, 201, 181, 181, 137, 111, 111, 55, 28, 28, 1, 137, 137, 137, 137] 201
rigid atoms, others: [39, 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, 40, 41, 42, 43])
total number of confs: 779
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052137 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052137
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052137/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052137
Building REAL300025052138
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052138'
/scratch/stefan/7786831/working/building/REAL300025052138 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052138

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052138/0 /scratch/stefan/7786831/working/building/REAL300025052138 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1056)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1056
`/scratch/stefan/7786831/working/3D/1056' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(O)=CC(Cl)=C2)CC1)

`REAL300025052138.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052138.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052138/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052138 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(O)=CC(Cl)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 12, 1, 1, 16, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
84  conformations in input
total number of sets (complete confs): 84
using faster count positions algorithm for large data
unique positions, atoms: [14, 14, 14, 25, 27, 36, 36, 36, 36, 36, 4, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 1, 1, 25, 25, 36, 14, 4, 4, 3, 8, 16, 8, 8, 1, 1, 1, 1] 84
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 140
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052138 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(O)=CC(Cl)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 12, 1, 1, 16, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
84  conformations in input
total number of sets (complete confs): 84
using faster count positions algorithm for large data
unique positions, atoms: [26, 19, 11, 1, 1, 1, 1, 1, 1, 1, 26, 26, 34, 36, 36, 36, 36, 42, 42, 42, 42, 42, 42, 42, 36, 36, 19, 19, 1, 26, 34, 34, 36, 42, 84, 42, 42, 36, 36, 36, 36] 84
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 234
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052138 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2=CC(O)=CC(Cl)=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 12, 1, 1, 16, 1, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
84  conformations in input
total number of sets (complete confs): 84
using faster count positions algorithm for large data
unique positions, atoms: [26, 26, 26, 37, 39, 42, 42, 42, 42, 42, 10, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 37, 37, 42, 26, 10, 10, 5, 1, 2, 1, 1, 8, 8, 8, 8] 84
rigid atoms, others: [33, 35, 36, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 37, 38, 39, 40])
total number of confs: 153
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052138 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052138
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052138/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052138
Building REAL300025052139
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052139'
/scratch/stefan/7786831/working/building/REAL300025052139 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052139

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052139/0 /scratch/stefan/7786831/working/building/REAL300025052139 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1057)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1057
`/scratch/stefan/7786831/working/3D/1057' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1)

`REAL300025052139.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052139.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052139/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052139 none CC(=O)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 4, 5, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 25, 25, 25, 86, 105, 200, 200, 200, 200, 200, 1, 1, 4, 5, 5, 5, 4, 4, 2, 7, 7, 25, 86, 86, 200, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 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: REAL300025052139 none CC(=O)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 4, 4, 10, 28, 28, 28, 95, 113, 201, 201, 201, 201, 201, 4, 4, 1, 2, 2, 2, 1, 1, 4, 10, 10, 28, 95, 95, 201, 4, 4, 4, 4] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 25, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 559
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052139 none CC(=O)C1=CC=C(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 200, 200, 200, 200, 146, 66, 66, 31, 66, 13, 1, 1, 1, 1, 1, 1, 1, 200, 200, 201, 201, 201, 201, 201, 201, 200, 146, 146, 66, 31, 31, 1, 200, 200, 200, 200] 201
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41])
total number of confs: 773
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052139 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052139
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052139/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052139
Building REAL300025052140
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052140'
/scratch/stefan/7786831/working/building/REAL300025052140 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052140

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052140/0 /scratch/stefan/7786831/working/building/REAL300025052140 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1058)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1058
`/scratch/stefan/7786831/working/3D/1058' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCC1)

`REAL300025052140.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052140.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052140/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052140 none N#CC1(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCC1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 10, 2, 2, 2, 1, 1, 1, 7, 17, 17, 17, 48, 75, 165, 165, 165, 165, 165, 1, 1, 15, 15, 15, 10, 10, 2, 7, 7, 17, 48, 48, 165, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15] 201
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 20, 21] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43])
total number of confs: 408
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052140 none N#CC1(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCC1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 7, 15, 15, 15, 15, 26, 49, 49, 49, 103, 139, 201, 201, 201, 201, 201, 15, 15, 1, 1, 1, 7, 7, 15, 26, 26, 49, 103, 103, 201, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 22, 23, 24] set([4, 5, 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, 36, 37])
total number of confs: 607
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052140 none N#CC1(CC(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)CCC1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 6, 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, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 165, 165, 165, 165, 137, 66, 66, 29, 66, 13, 1, 1, 1, 1, 1, 1, 1, 165, 165, 201, 201, 201, 201, 201, 165, 137, 137, 66, 29, 29, 1, 165, 165, 165, 165, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [33, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 822
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052140 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052140
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052140/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052140
Building REAL300025052141
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052141'
/scratch/stefan/7786831/working/building/REAL300025052141 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052141

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052141/0 /scratch/stefan/7786831/working/building/REAL300025052141 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1059)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1059
`/scratch/stefan/7786831/working/3D/1059' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052141.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052141.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052141/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052141 none C=CC(O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
327  conformations in input
total number of sets (complete confs): 327
using faster count positions algorithm for large data
unique positions, atoms: [109, 109, 60, 109, 60, 60, 60, 56, 48, 48, 23, 48, 13, 1, 1, 1, 1, 1, 1, 1, 60, 60, 109, 109, 109, 109, 327, 60, 56, 56, 48, 23, 23, 1, 60, 60, 60, 60] 327
rigid atoms, others: [33, 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, 34, 35, 36, 37])
total number of confs: 767
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052141 none C=CC(O)C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
327  conformations in input
total number of sets (complete confs): 327
using faster count positions algorithm for large data
unique positions, atoms: [28, 11, 2, 11, 2, 2, 1, 1, 1, 4, 16, 16, 16, 31, 36, 60, 60, 60, 60, 60, 1, 1, 28, 28, 28, 11, 33, 2, 4, 4, 16, 31, 31, 60, 1, 1, 1, 1] 327
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 20, 21] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 279
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052141 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052141
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052141/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052141
Building REAL300025052142
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052142'
/scratch/stefan/7786831/working/building/REAL300025052142 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052142

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052142/0 /scratch/stefan/7786831/working/building/REAL300025052142 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1060)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1060
`/scratch/stefan/7786831/working/3D/1060' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: [N-]=[N+]=NCCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052142.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052142.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052142/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052142 none [N-]=[N+]=NCCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.1', 'N.1', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [8, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 180, 161, 158, 75, 75, 75, 75, 60, 47, 47, 25, 47, 12, 1, 1, 1, 1, 1, 1, 1, 75, 75, 168, 178, 175, 175, 158, 158, 75, 60, 60, 47, 25, 25, 1, 75, 75, 75, 75] 201
rigid atoms, others: [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, 34, 35, 37, 38, 39, 40])
total number of confs: 871
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052142 none [N-]=[N+]=NCCCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['N.1', 'N.1', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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: [8, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [49, 49, 21, 14, 10, 2, 2, 2, 1, 1, 1, 3, 5, 5, 5, 16, 25, 75, 75, 75, 75, 75, 1, 1, 19, 20, 17, 17, 10, 10, 2, 3, 3, 5, 16, 16, 75, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 40, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 297
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052142 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052142
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052142/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052142
Building REAL300025052143
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052143'
/scratch/stefan/7786831/working/building/REAL300025052143 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052143

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052143/0 /scratch/stefan/7786831/working/building/REAL300025052143 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1061)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1061
`/scratch/stefan/7786831/working/3D/1061' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C)N1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052143.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052143.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052143/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052143 none CC1=CC=C(C)N1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 6, 19, 19, 19, 39, 47, 136, 137, 137, 137, 137, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 6, 6, 19, 39, 39, 137, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 46, 47, 48, 49, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
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: REAL300025052143 none CC1=CC=C(C)N1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 16, 16, 16, 33, 52, 52, 52, 110, 138, 201, 201, 201, 201, 201, 16, 16, 2, 2, 2, 1, 1, 2, 2, 2, 3, 3, 3, 3, 16, 33, 33, 52, 110, 110, 201, 16, 16, 16, 16] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 626
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052143 none CC1=CC=C(C)N1CCC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 137, 137, 137, 137, 88, 48, 48, 26, 48, 13, 1, 1, 1, 1, 1, 1, 1, 137, 137, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 137, 88, 88, 48, 26, 26, 1, 137, 137, 137, 137] 201
rigid atoms, others: [45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49])
total number of confs: 859
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052143 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052143
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052143/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052143
Building REAL300025052144
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052144'
/scratch/stefan/7786831/working/building/REAL300025052144 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052144

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052144/0 /scratch/stefan/7786831/working/building/REAL300025052144 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1062)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1062
`/scratch/stefan/7786831/working/3D/1062' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CN=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052144.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052144.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052144/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052144 none CC1=CC=CN=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 2, 2, 2, 1, 1, 1, 7, 20, 20, 20, 67, 79, 159, 159, 159, 159, 159, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 2, 7, 7, 20, 67, 67, 159, 1, 1, 1, 1] 201
rigid atoms, others: [43, 41, 10, 11, 12, 44, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 427
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052144 none CC1=CC=CN=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 23, 44, 44, 44, 106, 119, 201, 201, 201, 201, 201, 8, 8, 2, 2, 2, 1, 1, 1, 2, 2, 8, 23, 23, 44, 106, 106, 201, 8, 8, 8, 8] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29, 30, 31] set([8, 9, 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, 41, 42, 43, 44])
total number of confs: 594
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052144 none CC1=CC=CN=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 1, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 159, 159, 159, 159, 124, 61, 61, 29, 61, 13, 1, 1, 1, 1, 1, 1, 1, 159, 159, 201, 201, 201, 201, 201, 201, 201, 201, 159, 124, 124, 61, 29, 29, 1, 159, 159, 159, 159] 201
rigid atoms, others: [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, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 841
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052144 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052144
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052144/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052144
Building REAL300025052145
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052145'
/scratch/stefan/7786831/working/building/REAL300025052145 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300025052145

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052145/0 /scratch/stefan/7786831/working/building/REAL300025052145 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1063)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1063
`/scratch/stefan/7786831/working/3D/1063' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC[N@@H+]2C2CC2)CC1)

`REAL300025052145.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052145.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052145/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052145 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC[N@@H+]2C2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [11, 11, 11, 19, 21, 23, 23, 23, 23, 23, 5, 1, 1, 1, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 19, 19, 23, 11, 5, 5, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1] 23
rigid atoms, others: [11, 12, 13, 46, 47, 48, 49, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 91
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: REAL300025052145 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC[N@@H+]2C2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [23, 14, 9, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 14, 14, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 23
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46, 47, 48, 49])
total number of confs: 70
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052145 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC[N@@H+]2C2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 21, 22, 23, 23, 23, 23, 23, 6, 5, 3, 3, 2, 3, 2, 2, 2, 2, 1, 2, 1, 1, 1, 5, 5, 21, 21, 23, 15, 6, 6, 3, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 5, 5, 5, 5] 23
rigid atoms, others: [41, 42, 43, 44, 45, 20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48, 49])
total number of confs: 78
number of broken/clashed sets: 17
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052145 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC[N@@H+]2C2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 21, 22, 23, 23, 23, 23, 23, 6, 5, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 21, 21, 23, 15, 6, 6, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 5, 5] 23
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 80
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052145 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `1'
/scratch/stefan/7786831/working/building/REAL300025052145/1 /scratch/stefan/7786831/working/building/REAL300025052145 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 1 (index: 1064)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1064
`/scratch/stefan/7786831/working/3D/1064' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC[N@H+]2C2CC2)CC1)

`REAL300025052145.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025052145.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052145/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052145 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC[N@H+]2C2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 18, 19, 26, 26, 26, 26, 26, 5, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 8, 8, 1, 1, 18, 18, 26, 9, 5, 5, 3, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 1, 1, 1, 1] 28
rigid atoms, others: [11, 12, 13, 46, 47, 48, 49, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 110
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052145 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC[N@H+]2C2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [24, 15, 12, 1, 1, 1, 1, 1, 1, 1, 24, 24, 26, 26, 26, 26, 26, 28, 28, 28, 28, 28, 28, 28, 28, 26, 26, 15, 15, 1, 24, 26, 26, 26, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 26, 26, 26, 26] 28
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 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, 45, 46, 47, 48, 49])
total number of confs: 83
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052145 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC[N@H+]2C2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 22, 23, 28, 28, 28, 28, 28, 10, 8, 6, 6, 4, 6, 4, 4, 4, 4, 1, 4, 1, 1, 1, 8, 8, 22, 22, 28, 15, 10, 10, 6, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 8, 8, 8, 8] 28
rigid atoms, others: [41, 42, 43, 44, 45, 20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48, 49])
total number of confs: 98
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052145 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCC[N@H+]2C2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [13, 13, 13, 22, 23, 28, 28, 28, 28, 28, 8, 6, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 22, 22, 28, 13, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 6, 6] 28
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 112
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052145 /scratch/stefan/7786831/working /scratch/stefan/7786831
mkdir: created directory `2'
/scratch/stefan/7786831/working/building/REAL300025052145/2 /scratch/stefan/7786831/working/building/REAL300025052145 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 2 (index: 1065)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1065
`/scratch/stefan/7786831/working/3D/1065' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCN2C2CC2)CC1)

`REAL300025052145.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300025052145.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052145/2/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`2.mol2' -> `2.mol2.original'
`output.mol2' -> `2.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052145 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCN2C2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
159  conformations in input
total number of sets (complete confs): 159
using faster count positions algorithm for large data
unique positions, atoms: [16, 16, 16, 40, 60, 118, 118, 118, 118, 118, 5, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 15, 15, 1, 1, 40, 40, 118, 16, 5, 5, 3, 13, 13, 13, 13, 13, 13, 13, 15, 15, 15, 15, 15, 1, 1, 1, 1] 159
rigid atoms, others: [11, 12, 13, 46, 45, 48, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 315
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052145 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCN2C2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
159  conformations in input
total number of sets (complete confs): 159
using faster count positions algorithm for large data
unique positions, atoms: [73, 36, 13, 1, 1, 1, 1, 1, 1, 1, 73, 73, 108, 118, 118, 118, 118, 159, 159, 159, 159, 159, 159, 159, 118, 118, 36, 36, 1, 73, 108, 108, 118, 159, 159, 159, 159, 159, 159, 159, 159, 159, 159, 159, 159, 118, 118, 118, 118] 159
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 605
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052145 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCN2C2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
159  conformations in input
total number of sets (complete confs): 159
using faster count positions algorithm for large data
unique positions, atoms: [46, 46, 46, 84, 108, 159, 159, 159, 159, 159, 25, 15, 12, 12, 4, 12, 4, 4, 4, 4, 1, 1, 1, 1, 15, 15, 84, 84, 159, 46, 25, 25, 12, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 15, 15, 15, 15] 159
rigid atoms, others: [40, 41, 42, 43, 44, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48])
total number of confs: 466
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052145 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)C2CCCN2C2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
159  conformations in input
total number of sets (complete confs): 159
using faster count positions algorithm for large data
unique positions, atoms: [41, 41, 41, 79, 103, 159, 159, 159, 159, 159, 22, 13, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 4, 4, 13, 13, 79, 79, 159, 41, 22, 22, 9, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 13, 13, 13, 13] 159
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 469
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052145 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052145
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
2: /scratch/stefan/7786831/working/building/REAL300025052145/2.*
1: /scratch/stefan/7786831/working/building/REAL300025052145/1.*
0: /scratch/stefan/7786831/working/building/REAL300025052145/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052145
Building REAL300025052146
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052146'
/scratch/stefan/7786831/working/building/REAL300025052146 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052146

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052146/0 /scratch/stefan/7786831/working/building/REAL300025052146 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1066)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1066
`/scratch/stefan/7786831/working/3D/1066' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)COC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052146.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052146.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052146/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052146 none CC1(C)COC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 7, 32, 32, 32, 115, 151, 201, 201, 201, 201, 201, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 32, 115, 115, 201, 1, 1, 1, 1] 201
rigid atoms, others: [8, 9, 10, 43, 40, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 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])
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: REAL300025052146 none CC1(C)COC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 12, 42, 42, 42, 125, 155, 201, 201, 201, 201, 201, 4, 4, 2, 2, 2, 2, 2, 2, 1, 1, 1, 4, 12, 12, 42, 125, 125, 201, 4, 4, 4, 4] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 609
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052146 none CC1(C)COC1C(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 188, 83, 83, 30, 83, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 188, 188, 83, 30, 30, 1, 201, 201, 201, 201] 201
rigid atoms, others: [39, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 756
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052146 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052146
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052146/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052146
Building REAL300025052147
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052147'
/scratch/stefan/7786831/working/building/REAL300025052147 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052147

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052147/0 /scratch/stefan/7786831/working/building/REAL300025052147 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1067)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1067
`/scratch/stefan/7786831/working/3D/1067' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(N)C=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1C)

`REAL300025052147.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052147.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052147/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052147 none CC1=C(N)C=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 3, 3, 7, 7, 2, 2, 2, 1, 1, 1, 6, 21, 21, 21, 52, 61, 141, 142, 142, 142, 142, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 6, 6, 21, 52, 52, 142, 1, 1, 1, 1, 7, 7, 7] 201
rigid atoms, others: [43, 9, 10, 11, 44, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47])
total number of confs: 370
number of broken/clashed sets: 201
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052147 none CC1=C(N)C=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 22, 69, 69, 69, 133, 140, 201, 201, 201, 201, 201, 7, 7, 1, 1, 2, 2, 2, 1, 1, 1, 1, 7, 22, 22, 69, 133, 133, 201, 7, 7, 7, 7, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 25, 33, 26, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 646
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052147 none CC1=C(N)C=CC(C(=O)NC2(CNC(=O)CSC3=NNC(=O)[N-]3)CC2)=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 192, 201, 201, 201, 142, 142, 142, 142, 97, 45, 45, 28, 45, 13, 1, 1, 1, 1, 1, 1, 1, 142, 142, 201, 201, 201, 201, 201, 201, 201, 201, 201, 142, 97, 97, 45, 28, 28, 1, 142, 142, 142, 142, 201, 201, 201] 201
rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 686
number of broken/clashed sets: 201
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052147 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052147
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052147/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052147
Building REAL300025052148
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052148'
/scratch/stefan/7786831/working/building/REAL300025052148 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052148

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052148/0 /scratch/stefan/7786831/working/building/REAL300025052148 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1068)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1068
`/scratch/stefan/7786831/working/3D/1068' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CC=C(Cl)C=N2)CC1)

`REAL300025052148.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052148.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052148/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052148 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CC=C(Cl)C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 16, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 15, 35, 37, 85, 85, 85, 85, 85, 5, 1, 1, 1, 3, 3, 3, 22, 41, 41, 41, 41, 41, 41, 1, 1, 35, 35, 85, 15, 5, 5, 3, 22, 22, 41, 41, 41, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 307
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052148 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CC=C(Cl)C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 16, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [40, 25, 13, 1, 1, 1, 1, 1, 1, 1, 40, 40, 72, 85, 85, 85, 85, 186, 201, 201, 201, 201, 201, 201, 85, 85, 25, 25, 1, 40, 72, 72, 85, 186, 186, 201, 201, 201, 85, 85, 85, 85] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 766
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052148 none O=C(CSC1=NNC(=O)[N-]1)NCC1(NC(=O)CC2=CC=C(Cl)C=N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 16, 1, 8, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 114, 114, 186, 186, 201, 201, 201, 201, 201, 52, 41, 31, 31, 7, 31, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 186, 186, 201, 114, 52, 52, 31, 7, 7, 1, 1, 1, 41, 41, 41, 41] 201
rigid atoms, others: [35, 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, 38, 39, 40, 41])
total number of confs: 792
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052148 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052148
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052148/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052148
Building REAL300025052149
mkdir: created directory `/scratch/stefan/7786831/working/building/REAL300025052149'
/scratch/stefan/7786831/working/building/REAL300025052149 /scratch/stefan/7786831/working /scratch/stefan/7786831
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025052149

mkdir: created directory `0'
/scratch/stefan/7786831/working/building/REAL300025052149/0 /scratch/stefan/7786831/working/building/REAL300025052149 /scratch/stefan/7786831/working /scratch/stefan/7786831
Protomer 0 (index: 1069)
Found valid previously generated 3D confromation in /scratch/stefan/7786831/working/3D/1069
`/scratch/stefan/7786831/working/3D/1069' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=NC=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025052149.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025052149.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7786831/working/building/REAL300025052149/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052149 none CN1N=NC=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 8, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 13, 13, 10, 2, 2, 2, 1, 1, 1, 6, 12, 12, 12, 37, 56, 146, 146, 146, 146, 146, 1, 1, 13, 13, 13, 13, 10, 10, 2, 6, 6, 12, 37, 37, 146, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 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: REAL300025052149 none CN1N=NC=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 8, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 13, 27, 47, 47, 47, 102, 137, 201, 201, 201, 201, 201, 13, 13, 2, 2, 2, 1, 5, 5, 13, 27, 27, 47, 102, 102, 201, 13, 13, 13, 13] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 620
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025052149 none CN1N=NC=C1CC(=O)NC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 8, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 199, 146, 146, 146, 146, 123, 59, 59, 27, 59, 12, 1, 1, 1, 1, 1, 1, 1, 146, 146, 201, 201, 201, 201, 199, 199, 146, 123, 123, 59, 27, 27, 1, 146, 146, 146, 146] 201
rigid atoms, others: [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, 35, 36, 38, 39, 40, 41])
total number of confs: 850
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7786831/working/building/REAL300025052149 /scratch/stefan/7786831/working /scratch/stefan/7786831

Finished preparing REAL300025052149
Recording results
/scratch/stefan/7786831/working /scratch/stefan/7786831
Appending to /scratch/stefan/7786831/finished/xaaabbi.*
0: /scratch/stefan/7786831/working/building/REAL300025052149/0.*
Removing working files in /scratch/stefan/7786831/working/building/REAL300025052149
/scratch/stefan/7786831
Compressing combined databse files
/scratch/stefan/7786831/finished/xaaabbi.db2.gz
/scratch/stefan/7786831/finished/xaaabbi.solv.gz


=======================================================
WARNING: STORE_PROTOMERS not executable or a directory!
All results left in place (/scratch/stefan/7786831/finished)
=======================================================

Finalizing...
removed `/scratch/stefan/7786831/working/3D/1070'
removed directory: `/scratch/stefan/7786831/working/3D'
`/scratch/stefan/7786831/working/protonate' -> `/scratch/stefan/7786831/archive'
`/scratch/stefan/7786831/working/input-smiles.ism' -> `/scratch/stefan/7786831/archive/input-smiles.ism'
rmdir: removing directory, `/scratch/stefan/7786831/working/building'
rmdir: removing directory, `/scratch/stefan/7786831/working'
ls: No match.
ls: No match.